Prime Effect
by ApolloXL5
Summary: This is a Transformers Prime story that has been blended with Mass Effect. The story is set many years after the show would have finished and focuses on an adult Jack Darby. 15 years after the war had ended, newly promoted Commander Jack Darby joins the crew of the Autobot/Human Alliance frigate Normandy, just as a rogue Spectre is trying to unleash an ancient evil on the galaxy.
1. Chapter 1

A/N:** This is my first real fan fiction and I am attempting to blend Transformers Prime with Mass Effect, by mixing the characters (well getting rid of some and replacing others). The themes from Mass Effect will also be altered to fit more in tone with Transformers. But enough from me...**

**PRIME EFFECT**

**CHAPTER I**

Jack Darby looked out at the blue planet below him. It was the planet Earth, homeworld of Humanity. At this point he could see the continent of North America right below him, not a cloud in sight of the area of Nevada. Due to his learning of geography he could tell exactly where Jasper was. The town he had lived with his mother June Darby for most of his childhood. It had not been a very eventful life, his father left them both when he was very young and she found it hard to raise a son as well as work as a nurse at the local hospital. But Jack did not cause a single problem for her during this time. He was well behaved and always tried to help her when ever he could.

When he was 16 years old, he got himself a job at a local diner serving customers from the drive through section. It wasn't very good money and the customers always treated him badly (most of them were from his high school). But if it helped make his mother's life a little easier as well as put extra cash on the table then it was worth it. He had not always been so responsible, but when his father left he swore he would not become the same as him and so tried to be as responsible and compassionate as possible. June Darby was always proud of her son for that, even if she felt that he was growing up to fast and not enjoying his childhood.

Well the uneventful nature of his life changed the day he came across a blue motorcycle that would change his life in ways he had not imagined at that point. You see that motorcycle turned out to be an alien being known as a cybertronian. Her name was Arcee and she introduced Jack and two other human teens, Miko Nakadai a foreign exchange student from Japan and Rafael Esquivel a 12 year old boy genius to the rest of the Autobots. The group were made up of five transformers as the humans would call them. There was Ratchet, the team's medic who was always grouchy and always screaming "I need that" whenever one of his tools was broken by one of the bots. There was Bumblebee, the team's scout. He was the youngest member of the team and while immature for his age, he was a strong warrior. There was Bulkhead, the team's heavy hitter. He was once part of a group called the 'Wreckers', who were the Autobots black-ops team. Of course Arcee was the team's sharpshooter as well as the second in command. The one in charge of the group was Optimus Prime, he was noble and compassionate leader who believed that freedom was the right of all sentient beings.

The Autobots were on Earth defending Humanity in secret from the Decepticons who too were cybertronians, making this a civil war. The conflict had been going on for millennia and had left their own homeworld, a planet called Cybertron a dead husk floating in the blackness of deep space. The leader of the Decepticons was a bloody thirsty and ruthless cybertronian called Megatron. He was obsessed with bringing all life on earth and one day the galaxy under his own tyrannical rule.

As the human teens and the Autobots worked together, friendships blossomed among them. Bumblebee became Raf's guardian and closest friend. Miko befriended Bulkhead due to their joint love of rock music and destruction. Ratchet never thought much of humanity before he met the three teens, but they helped him to see past his prejudice and he began to see them as worthy allies. But out of the three friendships, Jack and Arcee were the closest. She was very cold to him originally, seeing him as nothing more than a mission and at most a burden. She had recently lost her partner Cliffjumper to the decepticons and was driven by the need to avenge his death. But Jack managed to help break down the wall of hate and self loathing that she had built around her spark and they grew closer. Jack and Arcee's friendship strengthened more after their encounter with Airachnid. A Decepticon who would be described best in human terms as a serial killer. Jack learned that she killed Arcee's partner on Cybertron, an Autobot named Tailgate. Jack managed to fight off Airachnid himself and gained Arcee's respect. She then considered Jack to be her new partner.

As the battle on Earth intensified, Team Prime came up against a number of threats. There was MECH, a terrorist group obsessed with gaining the transformers tech. Then there was Unicron the chaos bringer. A god like transformer who's body was at the center of the Earth. It was during this event that Optimus, who had been observing Jack through their time together and saw that the boy was fit to become the bearer of the Key to Vector Sigma. An ancient artefact that was connected to the matrix of leadership which Optimus carried within his chest. Unknown to Jack, Optimus saw that his responsible and compassionate nature gave him the potential to become a Prime himself, even though he was not cybertronian. Jack himself would not see this potential in himself for a number of years. When he finally did it was during the final battle of the war. He was 21 years old and by human standards was already a seasoned war veteran. Just not the war that humanity knew about, not before that day anyway. The battle took place in a number of cities between the Autobots and Decepticons. Megatron himself was attacking Washington DC and so Team Prime went there themselves while keeping in touch with their other allies fighting around the world. Optimus took Megatron on himself as Jack and Arcee provided backup. Megatron got the upper hand against the Prime until Jack threw an energon grenade at the Decepticon leader's right leg, crippling him. Optimus then ended the Con's life by ripping out his spark. The shock of Megatron's death demoralised the Decepticons and the surrendered to the alliance of Autobot and human forces who had fought side by side in the battle.

Ever since that day, nothing had every been the same. The Autobots and Decepticons had used up all of their energon reserves and so were no longer able to keep their bodies functional. They instead had to transfer their sparks into the human like pretender bodies that the cons had been building originally so that they could infiltrate human society . As a way to show appreciation for their efforts to save Earth, the leaders of the planet allowed the transformers to build a city for both species to live and work together in peace and they named the city New Iacon.

But after a few years Jack felt that he was no longer needed in the new Utopia that was being built and with Optimus's blessing joined the newly formed joint defence program. Arcee didn't take the news well but wished her close friend the best and told him she would wait for him to return. Miko joined the force too, but only so she could then work with Wheeljack, who had promised her a place among the Wreckers. Bulkhead had died during the war and Miko saw this as the best way to honour his memory.

Raf had decided to join the Autobot Science Foundation and Bumblebee stayed with him, loyal friend to the end.

Jack made few friends during his training, one in particular named Kaidan Alenko. And he was part of the reason why Jack was where he was now. He was aboard the Alliance's newest starship, The Normandy.

Jack looked away from the window when he heard voices approaching him from behind.

He turned around to see two men walking up to him, still talking to each other. One was an African-British man in his mid-forties. The other was a Caucasian man, who was in his early fifties but still in good shape considering his age. Jack recognised both of them. The former was Captain Anderson, the Normandy's commanding officer. The latter was Optimus Prime in his pretender body. Even after all these years Jack was still surprised whenever he saw the Prime.

"So this is the young officer that you wanted to have on my crew" said Anderson as he reached out and shook the young man's hand. "Its nice to meet you again Darby."

"Same here Captain" responded Jack. Optimus looked at both of them before speaking.

"Yes Jack has been a tremendous asset to my team during and after the war. And now that he is a officer in the Alliance, I believe that he could be of greater help to your ship and crew as it explores the uncharted areas of our galaxy."

Anderson took a moment and pondered on the Primes words.

"Well with your rank Darby you would become my XO. I hope you will be up to the challenge that goes with such a position."

A slight smirk appeared on Jack's face. "Yes sir, you can count on me".

"Good, well I am needed in the CIC, please join me there after you are finished with Optimus." replied Anderson as he headed to the elevator.

"farewell Captain " Optimus said. "Prime" Anderson acknowledged. As soon as Anderson was out of earshot Optimus turned back to Jack.

"So how have you been Jackson, it has been a while since we last spoke." Jack looked back out the window. "Well I suppose you heard about the incident on New Terra."

"Yes, the colony came under attack from a large force of slavers looking to abduct the colonists and killed the majority of the security personnel. It looked perilous for the families there. But you took command of the remaining soldiers and even though they were still inexperienced, you helped them keep their cool and successfully drove out the slavers with hardly any casualties to your group." Optimus recalled with pride in his voice. Jack didn't know where to look, suddenly feeling very embarrassed by the Prime's words.

"Yeah those kids did well despite the desperate situation we were in. But they really deserve the credit, all I did was not abandon them." Jack sheepishly replied. Optimus looked at him.

"You shouldn't be embarrassed by it Jackson, you showed them that they weren't alone and inspired them with the belief that they could overcome any threat or obstacle. That shows great leadership skill, and that again, you have proved me right that you have the potential to be a Prime one day. That was why I gave you the key to Vector Sigma all those years ago. I take it you still have the key on your person?"

Jack nodded and undid his uniform's collar button and pulled out a chain that he wore around his neck. On the chain and glowing ever so slightly was the key. It had shifted to the size of a pendant (like most cybertronian artifacts, it had mass shifting ability)

Optimus smiled at Jack. "I see that the key still resonates with you Jack. It takes a very strong spark or soul as your people call it to make the key glow like that." Jack put the key back under his uniform and buttoned his collar. He looked up and suddenly saw regret in the Prime's eyes. "Optimus what's wrong."

"Jack I am sorry I was not there for your promotion ceremony, I was forced to back out do to an incident between an Autobot transport and the Quarian Flotilla." Jack smiled and patted Optimus on the shoulder.

"Don't go beating yourself up Optimus, I know you would have been there if you could. Mom was there and recorded the whole thing. When next you see her, I'm sure she show you the video. She shows it to everyone."

"Optimus's face brighten up and he took a breath before replying. "I did hear about that and I will ask her the next time we meet." Jack raised an eyebrow at that comment. "How did you hear about it.

"From Arcee of course, she attended the ceremony. You didn't see her there?" Optimus asked curiously.

"No" Jack replied sadly as he looked away from Optimus for a moment, his memories of Arcee quickly overtaking his own thoughts. He had missed her as much as she was obviously missing him. But if that which had happened on the last night they were together had not occurred, then he might not have so readily accepted Optimus's suggestion to join the defence force. He faced Optimus, a little guilt showing on his face.

"I didn't know she was there. I mean we have messaged each other while I was training, but I haven't seen her since I left for basic training."

Optimus looked at Jack not quite sure as what to say. "Well I am not sure what had transpired between you two which has caused this predicament. But I think that whatever it is, you shouldn't let it get in the way of you friendship….." Optimus was about to say more when his com link activated.

"Optimus its Ratchet, the world leaders have asked to meet you in New Iacon at the Decagon about the new transit system we will be making available to them."

Optimus put his hand to his audio receiver. "Acknowledged Ratchet, I will be there momentarily." He then deactivated his com link and turned back to Jack. "It looks like I have to be on my way Jackson. If you ever wish to talk about anything that's on your mind, just give me a call." He placed his hand on jack's shoulder and smiled at the young man. "And I also want you to know that I am very proud of you."

"Thanks Optimus." Jack replied as Optimus smiled at him before turning away and entering the elevator, its doors closing behind him.

Once he was at the CIC Jack walked straight up to the cockpit and saw Anderson standing there talking to the pilot. Anderson noticed Jack and beckoned him over.

"Commander this is our pilot, Hotrod."

The pilot stood up and looked at Jack. He was a Caucasian male who looked to be in his mid twenties. He had orange hair with yellow highlights. He smiled and offered Jack his hand.

"Hi you must be Commander Jack Darby, it's a real honour to meet the human who helped put down Megatron."

"Thanks, so you are from New Iacon." Jack replied as he shook Hotrod's hand.

"Yeah, I was the one piloting the Ark when it landed on Earth years back. Elita One said I was one of the best pilots around so put my name down for this gig." Hotrod exclaimed proudly.

"Well its good to know that our ships is in safe hands Hotrod. Now if you will take us out of Earth's orbit, I want to see what the Normandy is capable of before we leave the Sol system. So we will be taking the ship on a shakedown cruise around the system." Anderson ordered as he beckoned jack to follow him back into the CIC. "Aye, Aye Captain"

Hotrod replied as he took his seat and started working the controls, taking the Normandy out of Earth's orbit and into outer space. Jack and Anderson stopped at the Captain's terminal next the galaxy map.

"So have you had a good look at the ship yet since you have been on board Commander? Anderson asked while looking over reports at his station. "Not really Captain, I came straight up here as soon as I boarded back at Earth." Anderson looked up at Jack. "Well then, since we are not leaving the system yet, i see no reason for you to be up here right now. Take a few hours off and take a look around. I'll call you if I need you up here." Jack saluted the captain and turned to leave. Anderson turned to Jack. "Commander, also your quarters are on deck 3 and your belongings are already there."

"Yes sir, thank you Sir." Jack replied. Anderson looked at him annoyed. Jack swallowed hard. 'G_reat, only been here five minutes and already irritated the Captain' _he thought to himself.

"And enough with the sirs, I like to keep things informal with my XO's ok?" he asked. Jack smiled and nodded. "Ok...Anderson" The captain returned the smile and returned to his station, leaving jack to his thoughts as he left the CIC.

In the hour or so after leaving the CIC, Jack had visited the engineering deck and Shuttle bay. He had met with the crewmen there. They all seemed like good, honest people who loved the job they each did. And he was pleased to meet each of them. But as of right now he just wanted to go to his quarters and relax until Anderson called for him. So Jack exited the elevator on deck three (crew deck) and made his way to the door to his quarters.

He opened the door and walked in. He was stunned by how large it was. It had a full sized bed, office desk and standard furniture. No bathroom, guess that meant he still had to share with the rest of the crew. But he was very impressed with it. The last digs he had was the top bunk in the crew quarters. he walked over and sat down on the chair and rested his arms on the desk. He then looked over to the personal terminal to his right and activated it. The blue screen lit up and displayed three options, messages, Journal and ship database. He noticed that he had one new message and selected it. His eyes widened at the name of the sender. '_Arcee'_ he thought to himself. He felt his heart skip a beat as he opened the message and began reading it.

Hi Jack, I know we haven't spoken for a long time but I hope that in sending this message to you that we can change that. I don't know how else to say this so I will just go ahead and say it, I miss you. Ever since you left it has not been the same without you partner. In the time after you gone Miko left to join up and Raf and Bumblebee soon after and it seemed that the Silo was more like a tomb than the happy home that it had been for the number of years since the three of you had come into our lives. Ratchet at first looked like he appreciated the quiet especially since it was usually Miko and her electric guitar giving him a headache as he tried to work on his experiments but now it looks like he misses the company too. As for Optimus' he just focuses on his work which as gone up a lot since the war ended. Funny, you would think that it would be the other way round. But I can see it is just his way of getting by. But myself, I have found it really hard to go on each day and not see your face smiling back at me when ever I go out for a ride on your motorcycle (which I have kept in perfect condition) or watch the sunset as we used to do. I have tried to keep busy but I find my thoughts always drift back to you. Jack I am sorry. If it was something I did I wish you would tell me. I mean very little has been said in the messages we have sent to each other in the past and I feel that we need see each other and get things straight.

So I hope you read this that you will at least consider us meeting up. I will be on the Citadel for the next week or so with Optimus. Apparently Perceptor is having a hard time with the council (once again it is the Taurian Councilor causing trouble for him), and I heard that the Normandy will be making a visit to the station in that time so I hope to see you there partner.

Jack sighed as he contemplated whether or no to answer. He then highlighted the respond button and was about to press enter when the ships intercom activated.

"Commander Darby, you are required on the command deck" A female voice spoke over the the com. Jack stopped and turned off the terminal, got out of his chair and straightened his uniform. "I'm on my way"

With that he left his quarters and headed to the CIC, leaving his thoughts of Arcee there in his quarters.

Jack entered the CIC as Anderson was standing over the galaxy map. He saw Jack and beckoned him over.

"Whats the situation Anderson" Jack asked, _'Still not used to that'_ he thought to himself.

" We are receiving a distress call from Ultra Magnus at the colony on Eden Prime." He turned to the yeoman. "Put it up on the galaxy map"

She worked away at her terminal. "Yes sir, I have worked it through several filters as it it is highly fragmented, probably due to enemy jamming".

"Ok show us what you have yeoman" Anderson replied as he and Jack watched the galaxy map change into the transmission as it began playing out in front of them. The image showed what appeared to be a battlefield with a man in red and blue armour talking in front of it.

"The is Ultra Magnus, autobot leader of the wreckers. The colony is under attack from the Geth, I repeat, the Geth are attacking the colony. We are outnumbered by superior forces and need assistance. Please hurry befo…" The transmission fizzled out and ended leaving all the bridge staff stunned. Anderson took a moment to ponder his thoughts before he straightened his uniform and composed himself.

" Hotrod, set course for Eden Prime and take us into the space bridge, set condition one through out the ship."

With that the lights around the CIC dimmed and the alert sounded around the ship. Everyone went serious and took to their stations. Anderson turned to Jack.

"Commander I want you and Lt Cmdr Alenko to suit up and prepare to go down to the planet as soon as we arrive. I will also place another soldier on your team. Your orders are to find Ultra Magnus and the rest of the wreckers and find out why the Geth are attacking the colony and help in any way you can."

"Yes of course Anderson" jack replied as he saluted the Captain.

"We will be the first ship on the scene. I know the Alliance will have be sending other ships too but we have to do what we can in the mean time." Anderson continued as he turned from Jack and walked away to the cockpit.

"Do you duty Commander" Anderson finished and Jack nodded and turned to leave the CIC via the elevator.

With that the Normandy flew up to the space bridge as it came to life with a massive bright portal expanding in all directions out of the device before the ship took off into it and out into the galaxy at beyond the speed of light.

**A/N: Well that was the first chapter, hoped you enjoyed it and let me know your thoughts either in reviews or PMs. Next time Jack meets an old friend from basic training and heads into battle at Eden Prime.**


	2. Chapter 2

**A/N: Well here is Chapter two, enjoy!**

**PRIME EFFECT**

**CHAPTER II**

The Normandy exited hyperspace and a shimmer glazed over it's hull as it entered orbit over a large planet.

"Captain we are in orbit over Eden Prime and the stealth system is activated. No Geth ships should be able to detect us." Hotrod explained to the Captain as he looked over the data on the pilot's display.

"That's good to know Hotrod. So are there currently any Geth ships in the vicinity?"

Hotrod worked the controls and another display appeared in front of him showing the planet and three red dots positioned around it. "Sir, there are currently three Geth cruisers orbiting the planet and they have shown no signs that they have spotted us".

Anderson stayed quiet for a moment as he took in the information given to him before activating the comm.

" Anderson to landing party, we are in orbit over Eden Prime. There are three Geth cruisers in orbit. To escape detection, I suggest your shuttle dives through the atmosphere and heads in low from the south and use the mountainous terrain to cover your approach."

In the shuttle minutes earlier Jack was sitting alongside two other soldiers. The guy sitting to his right Jack didn't know, but the guy to his left he knew very well.

"So we finally get an op together Darby" the raven haired young man said with a smirk.

"Yeah well we did make a vow during basic training to get put on the same ship eventually didn't we Kaidan." Jack replied with a smile. His friend chuckled at the comment. "We sure did, but we were just two raw recruits back then. Didn't realise how much crap we would see between then and now though right. I mean even after training we had numerous separate sorties against those Omega mercenaries and the Taurians while the Alliance was trying to be make peace with them, and then after those events you had to defend the colony on New Terra from those slavers by yourself and a few soldiers who were still green themselves." Jack took a breath as he recalled those memories. The battles flashing right before his eyes like they had happened only yesterday. He blinked, forcing the memories away and then smiled back at Kaidan.

"Its not like you had it that much easier, when you and your team were dropped off onto that uncharted planet only to come up against the Yahg." Kaiden rolled his eyes and laughed out loud.

"Oh god those things, they were ugly hulking brutes. And they have four sets of eyes, I certainly thought that hey look behind you wouldn't work."

The third man in the room who had been staring at Jack since they got into the shuttle not that Jack hadn't noticed suddenly jumped into the conversation nervously.

"So…um, is it always this relaxed when you head into a battle situation or is this just a good day."

Both men looked at him bemused, Jack actually surprised that the man could actually speak before Kaiden replied.

"You look nervous, is this your first op?".

The man wiped some sweat away from his forehead and nodded before carrying on fiddling with his hands.

"What's your name?" Jack asked gently. The nervous man looked up at him with an almost startled expression before clearing his throat. "Verner sir, Private Conrad Verner."

"Well private, you shouldn't worry. Since your on this ship my guess is that your good enough to be here. Plus you have me and the Commander here to watch your back." Kaiden added, giving Conrad a thumbs up. Conrad smiled back, looking a bit more relieved.

"Thanks" he replied before turning his attention to Jack.

"I would just like to say that it is a real honour to serve with the man that killed Megatron." Jack tensed up and crossed his arms, he never really liked having this kind of attention. "Thanks private, but I only helped end Megatron's life, I didn't do it my self." Conrad just stared at him intently, taking in every word that Jack said but not looking like he heard it properly. Jack just sunk into his seat and sighed, Kaiden noticed this and nudged his mate's shoulder. "Everything alright?"

"I'll tell you later" Jack replied before the shuttle's com system activated. Captain Anderson briefed them on the situation and the plan to get them down to the planet. Jack acknowledged and reported their status. "we are ready for launch Captain."

"Good Commander, we are opening the shuttle bay door now. Good luck."

The shuttle bay door opened to reveal the green planet of Eden Prime. The lights in the cargo area changed to red as the pilot called back to them. "Ok better strap yourselves in. High speed atmospheric entry can be quite nauseating". Jack, Kaiden and Conrad strapped themselves into their chairs as the pilot worked the controls and the Shuttle lifted off the bay floor and flew out into space, leaving the Normandy behind as it fired its engines on full burn and descended down to the planet below like a bullet.

Within seconds it hit the atmosphere causing the front of the shuttle (which has extra an layer of cybertitanium coated on the nose) to heat up at an extraordinary rate, causing things to get more than a little bit bumpy inside. As everything shook inside the shuttle, Conrad started feeling queasy and looked like he was about to spill his guts over the floor, until Kaiden got his attention. "Hey Conrad how many atmospheric dives is this for you?"

Conrad looked up, his face once again sweating and his eyes looking like they were screaming for it stop. "Four, simulated" he stuttered back nervously. Jack turned his head to him. "How many actual dives?" he asked curiously.

"One sir…..this one sir" he answered before he was forced to re-swallow the morning's breakfast back down his throat. Jack and Kaidan looked at each other and chuckled.

"Suck it up private, we're almost through the worst of it." Jack replied with a reassuring smile, which seemed to have had the intended effect on the private as he tried harder to fight the urge to regurgitate.

Suddenly the shaking subsided and the cargo area lights went back to white. "Atmospheric dive complete, we are good and in the mountains" the pilot informed them, as Jack un-strapped himself from his chair and got up to look out the main hatch's window. He could see that they were flying low to the ground with the mountains around them.

"Great flying ensign" Jack congratulated the pilot, who felt a proud smirk grow on his face.

"Yeah, that was the best dive yet, I didn't even notice what was happening this time" Kaiden remarked with a joking tone. Jack turned back to his squad who un-strapped themselves and stood up.

"Ok guys, check your gear, we'll be at the LZ in…", he looked back to the pilot who had heard him and replied. "Three minutes sir."

Jack turned back to Kaidan and Conrad. The former looking very happy with his weapon.

"You like your new rifle Kaiden?" Jack asked.

"You serious, this is the N7 avenger assault rifle. The newest gun to roll of the N7 production line." Jack picked up another avenger and looked at it.

"Wasn't N7 founded by Ironhide and your friend Rafael Esquivel sir?" Conrad asked Jack.

"Yes, Raf has a lot of projects on the go while he is working at the Ministry of Science in New Iacon. He messaged me a few days ago to tell me about our new armour that Mainframe and he had invented." Kaiden tapped Jack's shoulder pads, "Yeah our armour now has a small shield generator built into it and also the armour itself is made from a filtered cybertitanium alloy."

Jack handed a rifle to Conrad. "Which means we can take a few more hits than usual, but if your shield fails, don't take the risk. Get behind cover and wait for the shield to reboot."

Conrad nodded and held his rifle ready. Jack turned to Kaiden. "I just wish I had this armour a few years back." Kaiden smirked. "I hear that." The pilot turned to them. "We are at the LZ, ready?" Jack signalled the pilot who opened the hatch and the three of them jumped to the ground below, quickly regaining their balance and aimed the rifles ahead of them, scanning the area around them for hostiles.

"Clear" both Kaiden and Conrad called out and Jack acknowledged them before turning back to the shuttle which was hovering a few feet off the ground behind them.

"Ok we are going to head to the colony, you should head back to the mountains and lie low until we signal you for pick up."

"Acknowledged" The pilot responded before the shuttle rose in to the air and flew back towards the mountains in the distance." Jack turned back to his team.

"Ok our first objective is to reach the colony and make contact with Ultra Magnus." He then activated his holo-tool which lit up around his lower left arm and opened a screen showing a map of the area around them. Jack studied it and then looked back at his men.

"We are several clicks south of the colony, we will use this thick forest as cover as we make our way there. According to the Normandy's sensor sweeps, the Geth seem to be located around the North west area, while sending patrols through the rest of the colony to root out any resistance." He brought up the scan of the area surrounding the colony. " There is no sign of any Geth in the forest ahead of us." He turned off the holo-tool and re-equipped his weapon.

"You ready?" he asked both of them.

"Yes sir" they responded in unison. Jack smirked at them. "Ok, lets move out".

Dusk set over the planet's landscape as the Jack and his team made their way through the dense forest towards their destination. They had been walking for just over an hour, and were only a about two clicks out now. As they had traversed the forest, Jack had witnessed a number of the planet's creatures roaming the area. Intel stated that Eden Prime was not known for having any wild life that would pose a danger to humans which is one of the reasons the colony was set up. And the intel proved true as the animals Jack and his team encountered had kept their distance and just watched them for a moment before carrying on with what they were doing. _'Probably wondering what the hell we'_ Jack thought to himself as he saw a creature that looked somewhat like an earth deer, but with more of a serpent look, with scales instead of fur staring at him. Jack ignored it and carried on walking ahead of Kaiden who was scanning the distance for any enemies that they may have missed and Conrad bringing up the rear. Jack took a quick look at the private who had just slapped his neck in retaliation to a bug that had landed there. He lifted his hand off his neck and flicked it, sending the dead insect into the undergrowth beneath their feet. "Damn bugs" Conrad muttered to himself. Jack looked forward again and smirked. '_Talk about déjà vu' _he thought as he remembered the first time he went on a mission with Arcee, during his first year with the Autobots. They were investigating an energon signal that was deep in a forested area. Jack though was getting annoyed with the mosquitoes draining him of blood every few seconds. But by the end of that mission they had faced Arachnid and grown a little closer due to Jack's courage and compassion. Its funny how his thoughts would always drift back to Arcee no matter what was going on at the time. '_Ok, I will take her up on her offer and meet her at the Citadel after this mission'_ he finally admitted to himself. '_I don't know what I am going to say to her though…'_ He was snapped out of his thoughts by a the sound of rustling in the undergrowth just ahead of him.

He raised his hand and signalled his team mates to stop. They both looked at him confused, obviously having not heard the noise. Jack pointed over to the undergrowth in front of them, and gestured Kaidan to go round from the left and Conrad the right. Both men nodded and slowly and quietly went in those directions, circling the area that Jack had pointed too. With both men out of sight Jack slowly closed in on the area, making sure not to make any sounds as he lessened the distance between himself and whatever was making the noise ahead of him. He was just about on top of it when SNAP! He looked down and noticed a broken branch under his right boot. _'Scrap'_ but he carried on and closed the distance on the unknown. Holding the rifle, ready to kill if it was an enemy. But what he found was something else entirely.

He looked down on what had made that noise in the undergrowth. He was looking at a human woman in armour not unlike his own, but coloured pink and white. She was Japanese and had long raven black hair tied in a pony tail.

"Don't move" she warned him, panic evident in her voice, as she aimed her pistol at him, hands shaking slightly. "I'll shoot you if you come any closer."

"I wouldn't do that if I were you" Kaiden said as he and Conrad appeared both sides, weapons aimed at her. She looked around at them. Then it dawned on Jack who this was.

"Miko" he called to her, gaining her attention immediately. She narrowed her eyes at him as looked him up and down. Jack lowered his weapon and moved slowly towards her.

"Miko, its me Jack" he spoke calmly to her and approached her slowly.

"Weapons down" he ordered the men and they obeyed, lowering their weapons as Jack squatted in front of the woman. She lowered her weapon slowly too, though not sure why she was complying. Jack was no right in front of her and her eyes widened as it suddenly dawned on her.

"Jack" she happily exclaimed as she gave him a hug before a second later letting go and clutching her side.

"Your hurt, let me see that" said Jack as he examined her wound.

"Nothing some medi-gel couldn't fix" she replied as Jack pulled out a metal cylinder shaped apparatus and sprayed it over the wound, gaining an immediate relaxing look from Miko as the pain subsided.

"How did this happen, I thought you were with the Wreckers?" Jack asked concerned as he put the medi-gel away in the pouch on his belt. Miko sat up and pointed over to her right. Kaiden noticing this went over and found the corpse of a Geth lying face down in the undergrowth with a hole in its back. The body had a synthetic humanoid appearance except for the head which one would only describe as a flashlight head.

"Damn toaster was chasing me. You see our sensors detected an alliance signal for a micro second over the planet. Magnus knew it was help and sent me out here to meet up with whoever they had sent, knowing that any rescue would have to come via the mountains to prevent being detected by the Geth. I just didn't realise it would be you."

"Wait they sent you alone" Jack replied shock evident in his voice. Miko stared daggers at him. "I'm not kid any longer Jack, and you should know how good I am at stealth."

"Tell that to the Geth over here" kaiden remarked as he looked down at its lifeless body.

"That thing was already here, no one was following me from the base, I made sure of it." she replied irritably.

Jack smiled at her "Sorry Miko, I am just glad that you are alright, I still worry about you, you know" Miko calmed and returned the smile. "So, what kind of help have you brought other than the three of you." she asked.

"The Normandy is in orbit in stealth mode and we have a shuttle in the mountains waiting for our signal. But we need to get to the colony, what's the situation there?"

Miko activated her holo-tool and showed them the information on the screen it emitted.

"We have control of the south side of the colony and the Geth are holding the north side. But they are no longer attempting to come any closer. Almost like there is something in the North side that has their interest."

"Any idea what?" Jack asked curiously. Miko shook her head. "I don't know, you will have to speak to Magnus."

"Ok then" Jack replied as he stood up, helping her to her feet. "You alright to move?"

Miko padded herself down and holstered her gun. "Yeah, that medi-gel did the trick" she then turned around and walked over to the Geth corpse.

"You know, you will need more than just that pistol." Kaiden remarked. A confident smirk grew on Miko's face as she bent down and picked up the Geth's weapon and checked its ammo, before smiling back at Kaiden and Conrad. "I think I'm good, thanks"

"Ok then, Miko can you lead back to the colony" Jack asked as he held his weapon ready.

"Sure thing, follow me" she replied as she took the lead and the four of them headed further into the forest

By the time they had reached the colony, dusk had almost become night as the cloudy sky took on a dark crimson look above them. Miko had been right about the Geth staying on their side of the colony. They had not seen a single Geth centurion at all as they moved from one building to the next. The group came up to one building that looked almost identical to the others they had seen, save for the big metal doors blocking the entrance. Miko went up to the door and knocked on it several times, waiting a number of seconds before knocking it a final time. Jack had Conrad and Kaiden watch their backs as they waited for the doors to open, which they then did with a loud screeching sound. Miko then lead the group inside as the doors closed behind them. They entered a room filled with monitors with a man in blue armour with a red pattern standing in the middle looking at information on the screen in front of him. Miko stood to his side as he turned and looked at the new arrivals.

"Miko I see you were successful in your assignment" he stated with the same calm stoic presence that Jack would associate with Optimus. Jack stepped forward and shook the Wrecker leader's hand.

"Ultra Magnus, Commander Darby of the Normandy, we are here to assist you in reclaiming the colony." Magnus looked at the three of them before turning back to Miko.

"Gunnery Chief Nakadai, Wheeljack wished to know when you had returned, I suggest you go speak to him." Miko saluted him before giving Jack one last look and then leaving the room.

"Commander, I am glad you are here, the Geth have taken over much of the northern part of the colony."

Jack stood beside the man and looked at the monitor in front of them. "What is exactly in the northern side of the colony, civilian quarters?" Magnus shook his head. "No the civilians are locked in their quarters, to protect them. This part of the colony contains the labs where the colony's scientists work on the relics found in the dig site a few clicks to the west of the colony."

"Dig site?" Jack repeated. Magnus typed on the computer's keyboard and brought up images of the dig site and several artefacts that had been found. "The scientists believe that this planet used to be inhabited by the Lithone, an ancient bio-mechanical race not unlike how ours (cybertronians) used to be. But they died out 100,000 years ago by unknown reasons. Or so the scientist say."

Jack studied the images before turning to the Autobot. "why would the Geth attack the colony for a bunch of relics. I thought they hadn't been seen outside the outer rim of the galaxy for the last few centuries" Magnus deactivated the console and turned back to Jack.

"I don't know why they would be here now, but we have to stop them."

"I couldn't agree more" came a voice from the area where Miko had gone. Jack looked over to see Miko and a caucasian man in white and black armour with twin swords strapped to his back and two SMG's holstered to his belt. He had brown, wavy hair and a confident smile.

"Wheeljack," Jack smiled as the Autobot slapped his shoulder.

"Its been a while Jack. So I am guessing that between the two of us, these Geth don't stand a chance." Kaiden and Conrad walked forward and introduced themselves to Wheeljack as Jack looked back to the Wrecker leader.

"Well I think we have enough people here to make a run for the lab complex."

Magnus nodded in agreement. "If we split into two teams, one attacking the Geth head on while the other team can sneak in and finish this."

Jack nodded and looked at the people in the room.

"Ok, I'll take Kaiden, Miko and Wheeljack and we will attack their position head on. And private Verner will go with you" Conrad saluted at that, but Magnus shook his head. "I'll do better on my own." He was a bout to walk past when Jack grabbed his shoulder and stopped him. "I won't let you go out there alone." Jack replied with a determined look. "Conrad, you will go with Ultra Magnus and support him while the rest of us attack." Conrad readied his weapon and waited for the Wrecker leader, who picked up his Magnus hammer and holstered it on his back. He then turned to Jack with slight smile on his face.

"I can see why Optimus likes you Jack, alright I will follow the plan."

Jack smiled as the Autobot and Conrad left, only himself, Kaiden, Miko and Wheeljack remaining. He turned to them and readied his weapon.

"I hope you guys are ready for a fight. Because the Geth will have that lab heavily protected. We need to insure that we can keep the Geth occupied long enough for Magnus and Conrad to slip by unnoticed."

They all readied their weapons with confident looks on their faces. Jack smiled at all of them.

"Ok, lets move."

Jack's group had again not seen a single Geth as they made their way to the lab complex.

"I guess they really have got all their drones protecting the labs. I was at least expecting to kill at least a few of them before we get to the main event" Wheeljack said irritably as Miko walked beside him. "I'm sure there will be more than enough Geth for each of us to shoot once we get to there" she said reassuringly.

Jack signalled them to stop when he noticed something.

"What is it Jack?" Kaidan asked.

The Commander turned to them, his face questioning.

"Can any of you hear that?"

They all looked up suddenly when thunder and lightning blasted across the sky as the clouds parted to reveal a gigantic black alien ship descending over the colony. It was massive, with a shiny surface that looked like you would lose yourself in it if you looked at it too long. If Jack was to describe it, he would say that it looked like a some ancient monster from one of those old stories back home.

"What the hell is that?" Wheeljack asked in amazement at what he was witnessing.

"You haven't seen anything like that before?" Jack asked him back.

"No not in my lifetime and that is a long time" He replied not taking his eyes off the black ship.

Well whatever the hell it is, it is stationed itself right at the north end of the colony just beyond the complex. So lets keep moving" Jack said motioning them onward. Further away down the colony, the ship didn't go unnoticed by Ultra Magnus or Conrad who were quietly making their way to the lab.

The courtyard leading to labs was crawling with Geth centurions while Jack and the others hid behind a small wall and used it as cover at the far end. Jack peeked over the wall and saw not only centurions but also a cannon emplacement right at the entrance at the top the stairs which was high which gave the cannon the advantage of the higher ground and it would be able to fire at them no matter where they were in the courtyard.

"So how are we going to take out the Geth and that weapon emplacement?" Kaidan asked trying to sound confident. Jack looked back out to the Geth and smiled. The others noticed this and looked bemused at how their leader suddenly could smile despite the situation they found themselves in.

"I have an idea" he responded before he aimed his weapon and opened fire, causing the Geth to fire back, turning the courtyard into a battlefield.

Ultra Magnus and Conrad had made their way to the side entrance at far side of the lab complex that were guarded by just two Geth centurions who just stood there like statues. Weapons fire could suddenly be heard from the front of the building, making the Geth turn their heads towards the commotion.

As soon as he noticed this Magnus equipped his hammer and at first very slowly crept towards the two guards, making sure they did not notice him. When he was almost on top of them, he swung his hammer as hard as he could and smashed it into the head of the nearest centurion causing the flashlight it had for an eye to smash open spilling fluid out, staining the ground around them. The other Geth turned around and looked down at it's friend and then back up to the intruder with the large hammer. It then pulled out its weapon and aimed it at the Autobot, before having its head explode from a gunshot from Magnus's right. The body went limb and hit the ground, while Magnus looked to see Conrad with his rifle and smiled at the human.

"Nice shot kid."

The two of them entered the complex and searched each room, which was either full of cargo boxes or machinery. They came up to a large room with what looked like an large alien artefact in the middle of it, Magnus turned to Conrad.

"Hey kid, I want you out there and make sure no one enters this room, got it?"

Conrad nodded and headed out of the room. Magnus walked up to the artefact, fascinated by the patterns, the strange language that was carved on to it. He reached out with his hand and was about to touch it when the sounds of footsteps behind alerted him. He turned around Hammer in hand, ready to attack and stopped when he saw a Taurian in grey armour walking up to him.

"Saren Arterius" he asked, the surprise evident in his voice. The Taurian smiled at him. "I am here to help" he said in a calm tone as he walked past Magnus towards the artefact.

"I hadn't realised that the Council had sent a Spectre to help too" he replied. Saren stood behind Magnus and pulled out his pistol.

"I never said I was here to help you" he replied as he aimed the gun at the back of Ultra Magnus's head.

A gunshot alerted Conrad as he ran back to the room he had left the wrecker in and was shocked by what he saw. As he stood in the doorway he looked in to see the autobot lying on the floor dead with his head in a small pool of fluid. He looked up to see the Taurian staring at him. Conrad knew who it was, a million questions ran through his mind. '_Why is Saren here, why_ _is Ultra Magnus dead?'_ But before he could think of an answer Saren fired at the human, causing him to jump out of the way, training and instinct taking over as he rolled across the floor and ended up back in a kneeling position with weapon aimed right at Saren. But before he could fire a sound of something robotic approaching behind him caused him to turn and see a Geth centurion standing next him, weapon aimed right at him.

"Kill him" Saren ordered. Conrad knowing he was beaten, closed his eyes and waited for the inevitable to happen. The sound of a gun being fired echoed through the building.

The battle in the courtyard had heated up as Jack's team had taken out a number of the centurions but were still at a stand still due to the weapon emplacement.

"So I would love to know what this idea of yours is?" Kaiden asked impatiently. Jack smirked and looked at him.

"This" he answered as he placed one hand on the small wall they had used for cover. "Now cover me!" he shouted as he vaulted over the wall and fired his weapon riddling the Geth in front of him with bullets before charging off up the courtyard, the others didn't have time to be shocked as they fired their weapons at the Geth bearing down on the Commander who was still running through the battle, taking out enemies who got too close. Jack then saw his target and closed in on a Geth centurion who was carrying a grenade launcher. He pulled out his combat knife and sliced clean through the robot's left arm making it drop the weapon, before plunging the knife right into its eye, fluid squirting out onto Jack's face. He then noticed the cannon bearing down on him, so ducked behind cover while grabbing the grenade launcher off the ground next to its dead owner. He looked back to see his friends firing at the geth. He then summoned all of his courage to get up, aim the weapon and fire three grenades at the weapon emplacement causing it to explode in an amazing fireball sending the Geth around it into the walls of the building. At that moment the last Geth fell as his friends joined him where he stood. Miko looked at him and pointed at his face.

"I think you should clean that off" she suggested in a sisterly tone. Jack smiled and wiped the fluid off his face. Wheeljack and Kaiden looked at him impressed.

"Jack, who knew you had moves like that" Wheeljack said not hiding how impressed he was. "The last person I saw move like that was Optimus."

Jack suddenly felt embarrassed again. It happened every time someone compared him to the Prime. Changing the subject he pointed towards the complex.

"Well thanks but its not over yet, lets rendezvous with Magnus and Conrad and figure out what the Geth were after." The team then headed into the complex.

Once they were inside they walked through numerous labs and supply rooms looking for their friends, until they came to a large room with an artefact in the middle of it. On the floor was two bodies which all four recognised instantly.

"Magnus!" Wheeljack cried out as he and Miko rushed to side of the fallen wrecker, while Jack and Kaiden went to Conrad. But one look at the body gave them the unfortunate truth.

"He's dead" the Autobot confirmed as he reached down with his hand and closed the eyes of his old friend and Commander. Miko looked at the back of Magnus's head and noticed the bullet wound.

"Looks like someone got the drop on him" she said as she showed it to Wheeljack.

"Impossible, the only way that would happen is if it was someone he knew." Wheeljack replied as Jack and Kaiden looked over Conrad's body laying limp on the floor.

"I know who did it" Conrad opened his eyes and spitted out blood, gaining everyone's attention. Jack kneeled by him and got out the medi-gel, but Conrad stopped him.

"It's too late for me" as he gestured to the exit bullet holes in his chest.

"We cant just leave you like this" Jack argued back. But the private smirked at him.

"It was Saren Arterius, he has aligned himself with the Geth" he said trying to ignore the pain in his chest as blood continued to spill out despite Kaiden's attempts to stop the bleeding.

"The council Spectre with the Geth, that's impossible. Why would he even be here?" Miko asked confused.

Conrad used what strength he had left to lift his arm and point towards the artefact.

"He was after that, but had to leave when he heard your approach"

As if on cue, the thunder and lightning returned as Jack looked out of the nearest window to witness the giant black ship lifting off and back out into space. His com link then came to life.

"Commander Darby this Anderson, we have noticed that the Geth ships and one ship of unknown origin are leaving orbit, what is your status."

Jack put his hand to his com link in his ear and responded. "This is Darby, the colony is secured but we have one casualty, Ultra Magnus and one critically injured, Private Verner. We need pick up and will need the infirmary standing by"

"Understood, we have signalled the shuttle. It should be there in minutes, Normandy out"

Jack looked over to Kaiden who couldn't hide the sadness in his face as he looked at Jack.

"Conrad didn't make it." He said as he closed Conrad's eyes and stood up taking a deep breath. Jack walked over to him and placed his hand on his shoulder, giving him a sympathetic look. "He was a good soldier and he has just told us who did this. His death will not be in vain." Kaiden looked at Jack and nodded. The Commander then looked over Kaiden's shoulder and noticed Miko standing extremely close to the artifact which started to have a green glow around it.

"Miko I wouldn't stand to close to that."

Miko looked over to him before a she was hit by a green energy that was being emitted from the Artefact. Wheeljack looked on in horror as she was covered in the green energy before seeing Jack push her out of the way, the energy flowing over him instead. Jack found that everything went white. His whole body was in immense pain. Then it happened, the white light was replaced by a vision.

'There was fire everywhere, the environment around him was a smouldering ruin as Storm clouds raged overhead. The thunder deafened Jack as lightning flashed across the sky. The Commander looked around to find the bodies of aliens he had never seen before lying around him, hundreds, no thousands of bodies. It was a massacre of immense scale, then a familiar sound echoed behind him. Jack turned around to see the same massive black ships overhead firing extremely powerful looking red energy beams down at the planet's surface causing more devastation, then everything went black. If what he had seen had scared him, then what happened next caused chills right down to his soul. A ghostly voice spoke to him through the darkness.

"You have witnessed our end. Your end is about to begin. The Reapers are coming!"

**A/N: Well I hoped you enjoyed chapter two. Again please let me know what you think through reviews or private messages. Next chapter, Jack awakes from his nightmarish vision and arrives at the Citadel to tell the Council what he has found, as well as meet Arcee. Meanwhile Saren plots his next move.**


	3. Chapter 3

**A/N: Here is Chapter 3, enjoy! **

**PRIME EFFECT**

**CHAPTER III**

The Reapers are coming. That one sentence kept repeating in Jack's mind as he was surrounded by darkness. Usually he would be at peace with nothing around him while he slept, but this time was different. He had just been given a vision by an artefact that was built by an ancient race called the Lithone who had been wiped out 100,000 years prior by giant black ships which he assumed were the Reapers that the vision warned him of. But he found that the darkness around was not comforting, but cold and fearful and he wished that there was someone there to banish the loneliness he was feeling at this time, to tell him that everything was going to be alright.

He wished Arcee was with him. If there was one person in this life that could make him feel better, that could reassure him with the simplest of actions, such as smile it was his partner. But she wasn't there and that was his fault. Again he was reminded of that which he had pushed away all those years ago when he left. He wouldn't make that mistake again. He would fight to have her back in his life if necessary, and fight this new threat any way he could. But first he had to wake up. He willed himself to break free of the darkness around him and slowly but surely the darkness rescinded, replaced by light as he slowly opened his eyes and took a breath.

The brightness of the lights in the room dimmed as he eyes readjusted giving him chance to view his surroundings. He looked around and found himself to be lying on a bed in a room he did not recognise. A woman walked over to his bed side and looked down at him and smiled.

"I see your back with us Commander." she said in a friendly tone. He reached up with his left hand and rubbed his eyes as he tried to sit up, but then felt a hand on his shoulder gently stopping him.

"Easy, you have been unconscious for nearly four hours since you were brought on board"

Jack listened to her and lied back down. The woman went over to a work station and activated the com link.

"Captain Anderson, Darby is awake" she said. "You can come and see him now"

"Acknowledged Doctor Chakwas, I'll be down right away" came Anderson's voice over the com. The Doctor then returned to Jack who was starting to feel fidgety.

"Can I get up now?" he asked a little irritably.

"So you are one of those sort of patients then are you?" she asked jokingly. Jack looked at her confused. Now that his eyes were focused again, he could see the woman more clearly. She was a Caucasian woman in her mid fifties, but looked like she looked good for her age. Obviously she had taken good care of herself through her life. Jack could only hope that when he, or rather if he ever got to that age that he would look at least as healthy as she did.

"What kind?" he asked curiously.

"The kind that I will have to strap down to this bed to make sure that they don't move until I say that they can." she remarked.

Jack shrugged and looked at her. "Can I at least sit up, it feels like I have been lying down for long enough." Chakwas looked at him and then finally admitted defeat.

"Fine sit up, but don't get off that bed"

Jack the raised himself into a sitting position with his legs hanging off the side of the bed.

"Now that's better" he said feeling a little better. Chakwas then activated her holo-tool and ran it over the Commander, taking readings.

"So I take it your Doctor Chakwas, the ship's head physician. She nodded to him while continuing to take scans.

"Yes, and you are Commander Jack Darby, the Captain's new XO. Its a pleasure to finally meet you. I thought you would have at least seen me before you had gone off on a mission first mind you."

Jack smiled at her. "Sorry Doctor, when I looked around the ship earlier I would have seen you, but I was told you weren't here at the time."

"No, I was in the cockpit, treating Hotrod's headache" she replied, the irritation evident in her voice.

"Wait, Hotrod gets headaches, but he's Cybertronian. How does he get headaches?" he asked, his curiosity now peaking.

"Well the Cybertronians may be using pretender bodies now, but those bodies are bio mechanical in nature and were designed to mimic human physiology perfectly. So they are now susceptible to most none lethal ailments that we deal with everyday."

Jack was about to reply with another question when Anderson entered the Infirmary and stood next to him.

"How are you Jack?" he asked, once again in the informal way that Jack himself was still trying to get used too.

"I'm fine si….Anderson" he did it again, but if the Captain had noticed, he didn't let it show.

"No self diagnosis please, let the Doctor do her job if you will." Chakwas jumped in. She had just finished her scans and deactivated her Holo-tool as both men looked at her.

"Sorry Doctor, how is he?" Anderson asked.

"Well he is fine, physically and mentally. Whatever that energy was that hit him, has not damaged or effected him in any way that I can detect."

"Thank you Doctor" Anderson replied. Chakwas nodded and turned to Jack.

"You may return to duty Commander" she told him before turning and walking away.

"It was nice meeting you Doctor" Jack said with a smile, making her turn to him and return the smile before she carried on to her station. Jack then looked back at Anderson, who had a look of worry on his face.

"What happened to you when the Artefact hit you with that energy?"

Jack looked at Anderson and shook his head.

"I'm not entirely sure, I believe it showed me a vision, if that's the best way to describe it."

The Captain didn't take his eyes off Jack, listening to his every word.

"What did it show you?"

Jack closed his eyes and tried to remember the images that it showed him.

"I was standing in the ruins of a city with thousands of bodies lying around me, and then I saw a number ships that looked like that unknown ship that attacked the colony with the Geth. Then I heard a voice, and it said that I had just witnessed their end and ours was getting closer. The Reapers are coming. And then that was it."

Anderson saw Jacks face go slightly pale as he described the vision. "You think that giant black ship is what the vision was warning you of?"

"I'm not sure, but whatever it was, it was certainly powerful." Jack concluded.

"Well we will be arriving at the Citadel in the next few hours. The Council has requested us to give them a report on the Eden Prime incident. I think it is because one of our people has pointed the finger at Saren Arterius, the Council's most famous Spectre." Jack gave Anderson a determined look.

"Hey I may not have known Private Verner long, but it was long enough to know that he is no liar. If he said that it was Saren working with the Geth, then I believe him."

"Agreed, but we just have to hope that we can convince the Council of that." Anderson replied before turning to leave.

"Anderson, how are the others?" Jack asked gaining the Captain's attention again.

"Gunnery Chief Nakadia and Wheeljack are over in the common room. They have been quiet ever since we brought Ultra Magnus's body onboard. As for Lt. Cmdr Alenko, he was last seen down on the cargo bay. I had told them not visit you until you had been checked out, but since there is nothing to worry about, maybe you should see them before we reach the Citadel."

Jack nodded and got off the bed and walked out of the Infirmary with Anderson before heading to the common room.

Jack entered the Common room, it wasn't much really, just some tables with chairs as well as two sofas, one at each end of the room. He saw Miko and Wheeljack sitting opposite each other looking rather sullen.

"Hey guys" he said sheepishly as he walked over to them. Miko's face lit up as she darted over and gave him a hug.

"Jack, thank god you are alright, we thought you would never wake up"

After the embrace, they both sat down with Wheeljack.

"Yeah well some of us weren't so lucky" Jack replied sheepishly.

Wheeljack's eyes narrowed at the Commander's comment.

"Yeah well that will change as soon as I see that Turian bastard again. 'I'll carve Magnus's name into his chest as he dies."

Jack knew that Wheeljack and Ultra Magnus had a long history that started long before the war for Cybertron, but he could see where this was heading.

"Yeah, all we need to do is wait for that Turian to show his ugly mug and then put a bullet through it." Miko added enthusiastically.

Jack looked down at the table annoyed.

"Yeah because that worked well the last time didn't it." he muttered under his breath.

Miko having heard that looked at Jack.

"What did you just say?"

The Commander looked up to see both of them staring at him.

"Well remember Bulkhead and Hardshell." he said.

Both sets of eyes widened at the mention of Bulkhead's name and then narrowed at him as anger started to appear on their faces. Jack knew that Bulkhead was a sore subject, even after all these years, but he also knew he had to put an end to what ever they had planned so he continued.

"You killed Hardshell for what he did to Bulkhead, but what did it accomplish? It didn't help Bulk did it, he still died."

Wheeljack clenched his fist and slammed it into the table as his finally let his anger get the better of him. But rather than let the wrecker scare him, Jack stared directly at him. His face stoic and his eyes determined.

"Anger will not change that fact Wheeljack. Now if you want to remain on this ship and help me bring Saren to justice for what he did then I will happily accept your help. But I don't need nor want anyone on my team who as score to settle."

Wheeljack suddenly felt small in front of the human staring at him. God did this guy remind him of Prime. Jack then turned to Miko who was just staring at him, eyes wide, mouth slightly open. She had never seen Jack like this. She could now see why he now held the rank of Commander, and she suddenly felt a little better for realising it.

"Same goes for you too."

Miko nodded as Jack got up, slid his chair back under the table and walked out the room.

When Jack reached the cargo bay he found Kaiden leaning against the shuttle with a bottle of what looked like whisky.

"I hope you are not planning on drinking all of that now, especially since we are still on duty." Jack asked. Kaiden looked down at the bottle and then back at jack with a slight but sad smile on his face.

"Na, I was actually waiting for you to turn up. Glad to see your up and about." he said.

Jack stood beside him, arms crossed.

"So I'm here, what's up Kaiden?"

Kaiden bent down to a box he had next to his feet and pulled two glasses out of it and handed them to Jack.

"Well I thought we should share a drink in honour of Conrad."

Jack held the glasses as Kaiden opened the bottle and poured a small amount into both glasses, before putting the bottle down and accepting one of the glasses from Jack.

"He was certainly an interesting guy wasn't he?" Kaiden started. "With the motion sickness and his strange ability of attracting bugs to bite him."

Jack chuckled at that comment, reminding him of those particular moments.

"Yeah, as well as his fascination with me" Jack replied.

"Well the guy had a good taste in role models didn't he." Kaiden said casually.

Jack rolled his eyes at the comment. Again it made him feel uncomfortable. Kaiden noticed again and this time voiced his concern.

"That really bothers you doesn't it?"

Jack looked back at Kaiden and nodded.

"I guess that maybe I just don't feel like I deserve it." he replied as he looked down at his drink. "I mean there are plenty of other people out there that deserve that kind of attention."

Kaiden looked at his friend who was still looking away and thought about what he was going to say next, then smiled.

"Well its not every day that you discover an alien race, befriend them and then help defend the planet. Or even all the things you have done after you joined the defence force. But I tell you now, I know you deserve it. There aren't many people out there with the ability to inspire those around them the way you can Jack, and Conrad knew that too. Your exploits inspired him to join up and become part of something that was bigger than himself. You inspired those young men back at New Terra. Hell, you even inspire me Jack and I know you" he said with a smile on his face. Jack looked back to his friend, a lopsided grin growing on his face.

"Thanks Kaiden" he replied. He then raised his glass. "To Conrad Verner"

Kaiden raised his too. "To Conrad". Then both men then downed their drinks in one go. Jack started coughing as the strength of the whiskey hit him.

"That's good stuff" he coughed.

"Yeah it sure is" Kaiden replied chuckling at his friend's discomfort. "It's the Doc's, I sort of borrowed it while her back was turned. I intend on giving it back."

Jack having recovered, looked at him and shook his head at his friends confession.

"Still the same old Kaiden."

The Normandy exited the giant green portal of the space bridge and flew towards the colossal Citadel station as it sat nestled inside the gases of the serpent nebula. Jack observed the station from his room's window. He had seen many wonders during his life, and yet found he could still be surprised. The station was a marvel to behold, the nerve centre of galactic politics for the last several centuries as well as a massive city, home to over thirteen billion people from all over the galaxy. Now he was there to see the council and hopefully convince them that one of their most trusted Spectres had betrayed the values that they had entrusted him with. Jack knew that this was going to be a tough pill for them to swallow. Not only was it unthinkable, but the fact that it was humans pointing the finger too was not something they could tolerate. After all the Council saw humanity as a very young and brash race, not unlike Ratchet when he first met Jack and his friends. But they had managed to change the medic's view and Jack hoped that he could do the same for the council.

After the Normandy docked. The crew disembarked, Miko and Wheeljack heading for a club called Purgatory, obviously wanting to have a drink after the scolding the Commander had given them. Jack though was heading for the Council Embassies with Anderson and Kaiden. They had been told by a C-Sec officer that the Earth's political representative wanted to speak to them before he took them to meet the council.

After an elevator ride that felt like it lasted forever, they found themselves in the office of Donnel Udina. He had been chosen to be Earth's voice at the Citadel. Optimus Prime had not been in favour of this choice due to the man's obvious ambition for power. A trait that Optimus saw in Megatron when they used to be friends, but he let it pass due to Earth's leaders having the right to choose who should speak for them.

Jack saw the man standing next to the large windows that showed the rest of the presidium below them. Udina looked like a man that always had a lot on his mind. He turned to the three of them and he did not look happy.

"So Captain Anderson, I would say that it is a pleasure to see you again but that is not the case is it. Especially with the shit storm that you have brought with you." he said in dry tone underlined with a hint of anger.

"No I guess its not Donnel, but what we have to say to the Council is nothing but the truth." The Captain responded. Udina then looked at the Jack and Kaiden.

"So this is this must by Commander Darby. The one pointing the finger at the Council's precious Spectre."

Jack looked at him, the Commander's remaining stoic and calm.

"it's the truth, Saren attacked Eden Prime with the Geth and murdered two of our friends."

Udina looked like he was having none of it as he waved off what Jack had just said.

"You do know that those alien arseholes will not believe you, and I would rather keep my position if it is all the same to you."

Anderson walked right up to Udina and looked down at the old fool.

"I don't particularly care for you Donnel, I never really have. But if you are through with all the self whining, we would appreciate it if you took us to the Council now."

Udina did not know where to look, but shrugged and beckoned them to follow him.

Elsewhere on the Citadel, Optimus stood and looked out at the cityscape before him. Whenever he visited the station, he would always take the time to visit this spot and take in the view. After all it reminded him of Iacon, the city where he lived before the war that destroyed Cybertron all those millennia ago had happened. Back then he was a young clerk that went by the name of Orion Pax. Sometimes when remembering how simple life was back then, he found himself wishing that his life was still the way it was before he became a Prime. But unfortunately for him, fate rarely calls at a moment of their own choosing and what followed was meant to happen. The war that ultimately led to the fall of Cybertron and the exodus to Earth. And then only for the Decepticons to follow in their wake and prolong the war, with the future of the planet's original inhabitants at risk. But Optimus had found that the humans of Earth were not as easy targets for the Decepticons to conquer as Megatron himself foolishly believed. Because from that fateful day that the Autobots had met the three teens that had become like family to them in so short a time, Optimus could see what humans were capable of. There was Rafael who though was still very young, was so smart for his age, that he even gave Ratchet a run for his money though the medic never liked to admit it. Then there was Miko, she had an energy that never seemed to stop. She was impulsive and quick to action without a second thought. That many times caused the Autobots problems, but she had a strong and caring heart and still offered much to earth's newest residents.

Then there was Jack, if ever there was a person who the Prime would be proud to call a son it was him. For the young man was very much like Optimus, compassionate and courageous. He was always on hand to help whenever the Autobots had needed him. Then there was his friendship with Arcee, Optimus's SIC. Optimus had heard that she was not one for company after she lost her partner Tailgate. But when Cliffjumper had brought her to their base on Earth, he noticed that the femme had started to soften around the young Autobot warrior. Then that changed the day he was killed by Starscream. And she closed herself off from her family again, until she met Jack. And slowly but surely Jack's caring and compassionate nature managed to bring Arcee out of the dark and back into the light and their friendship strengthened as a result. Yes Jack was indeed a Prime in the making, even if the young man did not want to accept it, just like Optimus hadn't.

"Well I knew I would find you up here" a female voice said that caught Optimus's attention, making him turn to where it was coming from. There he saw a young woman walking up to him. She had pale soft skin and electric blue eyes. Her hair was blue with pink highlights that came down to halfway down her neck, and she was wearing a pair of jeans and a black T-shirt that complemented her athletic figure, Unlike most cybertronians, Acree did have a liking for human clothing. She stopped next to Optimus and looked out at the view, a happy smile on her face. Obviously she was happy and looking forward to seeing Jack after having received his message a few hours before that said they would meet up and she sure wasn't going to hide it.

"Well I like the view up here" the Prime answered.

"I can see why" she replied as she looked out at the city in front of her with the cabs flying past, going too an fro. Optimus then noted the time on his holo-tool and turned to the femme.

"Well now that you are here, we can head to the Council chambers in the presidium tower. Jack and Captain Anderson will be presenting their case against the Spectre Saren Arterius to the council members."

"Yeah sure" she replied happily. And the two of them made their way to the nearest elevator. As they walked through the garden like area around them, Optimus noted how this was the first time in years that he had seen his SIC this happy. He still did not know the reasons for her and Jack's uneasiness with each other and why the young man had chosen to take up the Prime's suggestion all those years ago. But he wasn't going to pry, he would wait for them to open up to him when they felt ready to do so. Of course their seeing each other here on the station could also bring their problems to a close and that would also be good.

"So how are you Optimus?, Ratchet told me that the Quarian situation had gotten a bit strenuous." Arcee asked seeing the thoughtful look on his face.

"I wish I could say that it was a minor misunderstanding Arcee. But one of our transports had gotten to close to their Flotilla and they sent out some of their patrol fleet to warn our ships away. It would seem that they still do not trust us."

Arcee looked at him confused, trying to read the Prime's thoughts.

"But why, we are nothing like the Geth. Those robots were built by them, we didn't have the same kind of origin as them, hell we weren't built by anyone." she questioned, irritation evident in her voice.

"I tried to reason with them as such when I spoke to Admiral Raan over the com channel back at New Iacon. But she wouldn't have it, she said that if one of our ships ever happened to be in the same system as their flotilla, then it would be destroyed. I fear that we may never be able to gain their friendship."

Arcee saw the disappointment in the Prime's face and thought it was best to try and cheer him up.

"Come on, lets go see Jack and watch him show those councillors whose boss"

The Prime looked down at the femme and saw the infectious smile that had appeared on her face and could not help but smile back. He nodded and the two of them entered the elevator and headed up to the Council Chambers in the tower above them.

**N/A: I hoped you enjoyed that, because I enjoyed writing it. I am sorry that I didn't get to any of the events that I said I would, but I just found myself wanting to write about how the characters dealt with the fallout of Ultra Magnus and Conrad Verner's deaths. Again let me know what you thought of this chapter in reviews or PM's and thank you for reading. ****  
**

**In chapter 4, jack makes his case to the council, meets a certain token Tauran C-Sec officer and helps save a young quarian.**


	4. Chapter 4

**A/N: Here is the next chapter, enjoy! **

**PRIME EFFECT**

**CHAPTER IV**

As Optimus and Arcee entered the Citadel Tower, Acree was amazed by the beauty of the gardens and fountains that made up the area that lead to the Council chamber. As she looked around she saw many people of different races walking around the area or sitting on the benches talking to one another. She unintentionally overheard a conversation between a Turian and Salarian discussing the chances of a Volus getting a seat on the council.

"No chance there" the Salarian replied. "The Volus would need a ladder to reach the seat" gaining a laugh of approval from the Turian. Acree frowned at the remark. She didn't like people who made fun of others for their differences, no matter what they were.

For her back on Cybertron it was due to her lack of height back when she had her old body. The bots would make fun of her and she always snapped back at them. She was temperamental that way. But when the war started she used what many considered to be weakness to great effect as a sharpshooter and scout, being able to sneak in and out of places undetected was an advantage that the Autobots could not afford to waste. And also with her combat training curtsey of Prowl. Who was a master of circuit-su, the Cybertronian equivalent of martial arts. Arcee became a weapon of war on the battlefield. He taught her to use her small size and quick speed to devastate those who were larger and slower than her, and as time went on she did just that. But she wasn't the only one to prove true her belief, there was also Jack who time and again during the twilight years of the war proved how much of a danger they could be to those who underestimated them.

When they were further away from the pair of idiots as Arcee thought of them, she caught sight of a monument in the center of the main garden display. If she was not mistaken, it looked just like a space bridge.

"I see you recognise it Arcee" Optimus observed as she studied the monument.

"Why would they have monument to space bridges here?" the femme asked.

"No one really knows, since it has always been here since the Citadel was discovered by the Asari several hundred years ago."

He was about to continue talking when they saw that the Council meeting was about to start and so headed on in.

When they entered the council chamber, Optimus and Arcee found a spot on one of the upper floors and stood at the balcony which gave them a great view of the whole chamber. As the femme looked around, seeing that quite an audience had gathered for this meeting, looking down from adjacent balcony's on the other side of the chamber. She looked down to see the Councillors themselves standing at their podium. There was an Asari, a Turian and a Salarian and of course she would recognise Perceptor, who was the Cybertronian Councillor. He looked like he didn't want to be there and when she looked up at Optimus, she noticed the same worry on his face as he looked down at the other Councillors.

"Whats wrong?" she asked.

"I can already see that this will not go well Arcee, I can tell that just by looking at Perceptor."

The femme was about to speak when from the corner of her eye she spotted someone. A young man she would never forget, he was dressed in the standard alliance uniform and he looked rather good in it if she did say so herself. It was her partner, her Jack.

Jack walked into the Council chambers with both Anderson in front and Kaiden to his left and Udina following behind them. They crossed the bridge to the box in the centre of the chamber as the Council members stood before them. The massive pane glass window behind them bathed the councillors in light, almost making the four of them look like gods up there on their podium. Jack remembered back to Arcee's stories of the High Council back on Cybertron before the war, they too were described as just as illustrious. But he wasn't going to be intimidated here, he had a job to do and he was going to see it through.

"The council would like to welcome you to this meeting Captain Anderson" Tevos the Asari Councillor said trying to sound as pleasant as possible.

"Thank you for seeing us today madam Councillor" the Captain replied. But before he could say anymore, the Turian councillor jumped in.

"Can we stop with the pleasantries and get down to the reason why this meeting was called for today" Sparatus said.

"Yes we would really like to know why you believe that a Spectre as honourable as Saren Arterius would commit an atrocity like what happened at Eden Prime." Valern the Salarian Councillor asked.

"Councillors, please show some restraint and give them some room to breath before you start attacking them with questions." Perceptor said trying to use reason.

Sparatus glared at the Autobot.

"Why, how would you feel if someone came in and tried to blame a heinous crime on your own Optimus Prime, I have every right to be angry. Saren is a good friend of my mine and I will not see his name being tarnished by humans."

The Asari councillor turned to the Turian.

"Then maybe you should exclude yourself from this meeting, we should at least hear them out first, no matter how ridiculous their claims may lead to be."

Jack looked up at the councillors bickering between each other and couldn't help but smile slightly. Doesn't matter if you are on Earth or at the far end of the galaxy, politics was politics wherever you went.

"Very well, please come forward and deliver you evidence." Sparatus said after he calmed down.

With that Jack stepped forward.

"And who are you?" Sparatus asked not even trying to hide the disinterest in his voice.

"Commander Jack Darby, Alliance Military" the young man answered stoically.

"Welcome Commander, please give us your account of what happened." Tevos encouraged in a friendly manner.

So Jack and then Kaiden began giving their accounts of what happened on Eden Prime, from the landing on the planet and battling the Geth to the mysterious black ship that appeared over the colony, the latter being dismissed as a Geth ship.

Arcee looked down from the balcony with Optimus as the meeting continued, watching as Jack gave his account of the events. He was so confident and mature, not that he wasn't always like that. It was just that he seemed so much more sure of himself. She found herself entranced by Jack as he talked, a feeling coming over her that she had not felt in a long time. Not since the night he left, and she still was not entirely sure what the feeling was. Optimus had noticed the femme's attention had been solely on Jack this entire time and smiled. He finally started putting the pieces together to the puzzle that was Jack and Arcee. He knew that they had been extremely close, but seeing this behaviour from his SIC had confirmed it. The only mystery now left to solve was what had happened between them years ago. He opened his mouth to speak to the femme, when he noticed her relaxed face suddenly become serious as she looked out to the other side of the chamber.

"What is it Arcee" the Prime asked.

"You see that Turian over there, the one in the blue and black armour. Isn't he acting like he has a lot riding on this meeting?" she asked.

Optimus looked over to see a Turian with blue face paint and a visor over his left eye. He was watching the meeting below and did not look happy with how it was proceeding. And after a few more minutes he had had enough and walked out. Optimus turned back to the femme.

"Yes Arcee, he did look somewhat disturbed by the proceedings." They both looked back down to the council meeting below them, Arcee's attention returning to Jack.

"That is the most ridiculous story I have ever heard and you don't even have any real proof." Sparatus spat back at Anderson and Jack as the two of them stood there looking back at him.

"Please calm down, this isn't getting us anywhere." Perceptor pleaded. But the Turian was having none of it.

"I would have to agree with Sparatus, Captain Anderson and Commander Darby unless you can bring us real evidence to back up your claims, then there is nothing we can do. I am sorry, and this concludes this Council meeting."

And with that, the councillors started to leave, the Turian storming out first. Perceptor was about to leave but not before looking back at the humans and giving them a sympathetic look and then like the others he was gone. The audience that had watched the whole thing had upped and left too, leaving just Optimus and Arcee who watched as the human trio turned and left in defeat.

"Come Arcee, we shall go and offer our support to Jack and the others" the Prime said. Arcee nodded and the two left the now empty Chamber.

Once outside and back in the calming environment of the gardens, Anderson turned to his two officers.

"Well that went well" he said trying not to sound too sarcastic.

"Your telling me, they were never going to believe us in the first place. Which made this whole meeting a waste of time." Kaiden replied, not even hiding his anger.

"Well until we have solid evidence, I guess there is nothing we can do" Anderson said.

Jack stayed quiet the entire time the two were talking, trying to think of something that could help them. He was about to speak up when another voice was suddenly heard from behind him.

"Maybe I can be of some help?"

The three of them looked over to see a Turian approach them. He was wearing C-Sec armour and had a visor covering his left eye.

"And you would be?" Kaiden asked.

"Garrus Vakarian, I am with Citadel Security"

The three men looked at the new arrival, trying to work out whether this was real or not. But Jack stepped forward and offered the Turian his hand.

"I'm Commander Jack Darby." he said in a friendly tone and with a slight smile.

"it's good to meet you Commander" he replied as he noticed Kaiden staring at him with distrust." I guess you would like to hear how I can help"

"Oh we are all ears" Kaiden remarked sarcastically. Jack glared at him, making the Lt Cmdr suddenly feel very small. This had not gone unnoticed by Anderson who watched as his XO and the Turian began to talk.

"Well how can you help us then?" Jack asked. Garrus activated his holo-tool and showed them a number of reports.

"Well I was recently running an investigation into the Spectre Saren Arterius, due to some very disturbing reports of his activities in the Terminus systems, but I found that I was being blocked at nearly every turn. You know sometimes giving Spectres free reign across the galaxy can be a real pain in the ass. Especially when that Spectre is playing everyone for fools"

"What makes you say that?" Jack replied. Garrus showed them some more intel on his holo-tool's screen.

"Well like I said, I keep getting blocked at every turn, but there just is something not right about that Spectre. But I do have one lead."

"What's that then?" Jack asked, his attention fully on what Garrus was telling them.

"I know a Krogan Bounty hunter, who goes by the name of Wrex down on the lower levels, that has come across some information about Saren."

"Well what kind of information" Kaiden asked.

"He wouldn't say over the com, he would rather meet face to face and down on the lower levels. And with how C-Sec doesn't have that much control down there. I feel it would be better to go down in greater numbers than just one." Garrus told them honestly.

Jack turned to Anderson.

"Captain, I think this worth investigating."

"I agree Commander, ok you and Alenko will assist Mr Vakarian here in getting that proof and bring it back to the council while I head back to the Normandy and report the days events to our superiors"

Anderson then offered them a supportive smile before turning around and heading to the transport back to the Presidium.

Garrus then stopped the two men as they were about to head to the transit hub.

"What is it Garrus?" Jack asked confused.

Garrus looked them both up and down.

"Don't you two think you two should be wearing something a little less conspicuous, Alliance military types are not well known for walking around with the lowlifes."

Well what about you, don't tell me that you can go in dressed like that?" Kaiden asked surprised. Garrus gave him a knowing smile.

"Well its like I said, a C-Sec officer isn't even a blip on the radar of the guys down there, maybe because my superiors are busy being paid off." he answered, the last part had a tinge of anger to it. "But if we come across any trouble I can easily handle myself."

"That's good to know" Jack replied with smile. "Ok if you know where we can get clothes to better blend in with the lowlifes down there, then lets get going."

"I know just the place" Garrus finished as the two humans followed him to the transit station.

Optimus and Arcee had just re-entered the gardens when they noticed Jack, Alenko and that Turian from earlier get into a cab and watch it fly off to another part of the Citadel.

"Well that is unfortunate" The Prime said sadly. He then looked at Arcee and noticed the intent in her eyes as she looked at the transit station.

"You want to go and help Jack don't you?" Optimus said bluntly, causing the femme to look up surprised.

"Am I that easy to read?"

"Not at all Arcee, but I do know you well enough to see when you have made your mind up about something." he replied as he smiled at her. She sighed as his words hit home within her spark.

"Yes I want to help Jack, I want to help my partner." she answered truthfully.

"Then I will take my leave and go and see Captain Anderson" the Prime replied as he turned and walked away before turning to his SIC one last time.

"Arcee, be careful and good luck"

She smiled and nodded at the Prime, her smile saying a silent thank you to her friend and Commander before heading off to the transit station to follow her partner where ever he was going.

The trip in the transit cab was not a very relaxing one for Arcee. Mainly due to the fact that she spent the whole time thinking about Jack. As she looked out of the side window at the sky scrapers that flew by as the cab followed the same path as Jack's one, she thought about how much he had changed since the last time she had seen him. Well she was thinking of the very last time she had seen him years ago, but she did recently attend his promotion ceremony, where he was given a medal for his part in the defence of New Terra and was also promoted to Commander. It had surprised Arcee how fast it had taken Jack to rise up the ranks. For herself it had taken several vorn to reach the rank of commander. So for the young man to reach it in a fraction of the time was something to be proud of. If only she had gone up to meet him then and tell him how proud of him she was. But at that moment she felt that if she was to surprise him like the way she had the night he had left, that it would have ended in a similar fashion. Remembering that night made her spark ache, so she did her best to expel those thoughts from her mind as she looked out at the city expanding down one of the arms of the Citadel. It growing larger as the cab descended into it.

Down in the under city of the Citadel, two men and a Turian walked down one of the many dark and trodden streets that littered the foundations of the massive station. As they walked through the crowded streets, the two men did not look any different from anyone else that was there. Kaiden was wearing a baggy pair of jeans and a grey hoodie, while Jack was wearing a similar set of jeans, but instead of a hoodie, he wore a dark green T-shirt with a black biker jacket. Kaiden gave Jack jealous look.

"Why did you get first choice?" he asked. Jack looked over to him and gave him a lopsided grin. "Maybe because I am the Commander."

Kaiden muttered something that Jack did not hear clearly, and just assumed that it was an insult. But he just ignored it and looked ahead to Garrus, who was still wearing his C-Sec armour. But true to his word, no one around here had even batted an eye lid at him. '_I guess the lowlifes really do run things down here_' he thought to himself as he looked around him to all the shady people that were crowding the streets.

"So where are we going exactly?" Jack asked to the Turian in front of him.

"Well, Wrex told me to meet him at the End of Days club just down this street."

"We are meeting him at a bar?" Jack asked curious about the location. Kaiden having heard Garrus perked up. "You read my mind, I was just thinking that I would rather be drinking after what we just went through upstairs". Garrus chose to ignore the man and carried on talking to Jack.

"Well he is a Krogan and he likes watching the dancers, plus it is about the only bar left on the Citadel that hasn't banned him."

"Charming" Jack replied as they came up to the entrance to the bar. It was covered in violet and blue neon lights and had two Batarian bouncers guarding the doors. Garrus turned to Kaiden and Jack to do some final checking.

"Now you both have the pistols I gave you right?" he said while looking like he was handing out credits to both of them as the bouncers looked over curiously.

"Yeah we have them hidden, think we will need them?" Jack asked as he pretended to accept the creds.

"Hard to say." He then took a breath. "Right then shall we"

With that Garrus and the humans walked past the bouncers and into the club. Not a second had past that another group of men, well armed by the looks of them walked out from the shadows and entered the club after them. Had they checked their surroundings first, they may have noticed a pair of electric blue eyes that had been watching them from further in the shadows, a stern look growing on her face. Only one thought entering her mind. '_Jack!'_

If it looked like the place was crowded on the outside, then it was heaving inside. There was barely room to breath let alone move as Jack, Kaiden and Garrus tried to squeeze past all the bodies in the club. The neon lighting inside was almost as bad as it was outside. It was starting to give Jack a headache. He would rather spend a quiet night watching the sunset than have his eyes and ears physically abused by the lights and sounds of these types of places. The music was a one note, tone deaf assault on the senses. He was suddenly pulled from his thoughts when Garrus tapped him on the shoulder and pointed to the large Krogan in red armour sitting at a table with an Asari Dancer on top of it, holding onto the pole going through the middle of the table. He was drooling over the girl as she thrusted herself into the pole before bending over backwards and smiling at the hulking brute while giving him a good view of her large breasts that were nearly bursting out of her skin tight outfit.

"Very nice" he slobbered as Garrus and Jack approached his table with Kaiden behind them.

Wrex then spotted the group as they neared, his reptilian eyes narrowing until he recognised the Turian and smiled.

"Garrus, you old pyjak" he said as the dancer noticed the group and decided to leave, taking a tip from the Krogan before disappearing into the crowd.

Both men shook hands before Garrus took a seat next to him.

"I figured you would have been kicked out of this place by now, going by your current track record."

The Krogan gave a hearty laugh.

"Yeah well that doesn't usually happen until I am on the eighth bottle of Ryncol, then I start trying to touch the dancers."

Garrus looked over Jack and grinned.

"Its true, he is like a newborn baby, hands everywhere." Garrus joked, gaining a slight smile from Jack. Wrex looked over at the strangers.

"Garrus, who are these pink skins?"

Jack offered the Krogan his hand.

"I'm Commander Jack Darby" he said with a smile. The Krogan just looked at it and scoffed, making Jack feel a little nervous.

"Hey these guys are ok, in fact they are with me because of the intel you have on Saren"

The Krogan suddenly looked serious as he looked around them before speaking.

"Well it's not so much intel as it is a person."

"What do you mean?" Jack asked, edging closer.

"Well I ran into this Quarian a few days back, poor thing looked like she had been running for a long time. She saw me and probably thought that I could protect her and so asked for my help. She said that she had stumbled onto some information while on her pilgrimage. Then next thing she knew, she was being chased by mercenaries."

Jack and Kaiden listened to every word that Wrex told them before speaking.

"So where is she, we could really use the information she has."

Wrex pointed up.

"She's upstairs, I have been hiding her here since I found her. Gave her some first aid too, since she had been shot when I found her."

Jack stood up and tidied himself up.

"Can you take us to her now. We can pay you whatever fee you want and place her into protective custody once we get her back to the presidium."

The Krogan looked both men up and down and scoffed again.

"You, what makes you think you can protect her?"

Garrus nudged Wrex's shoulder and whispered something into his ear.

"That's him, the hero of New Terra and the man that helped kill the Decepticon leader Megatron. Well now, why didn't you just tell me that to start with." he chuckled as he got up and lead the three of them up the stairs. He lead them to another room that was only half the size of the club below and they saw the Quarian sitting at a table, her body language looking rather nervous. This was the first time that Jack had seen a Quarian. She was wearing a black and purple enviro-suit with purple hood covering her breather helmet that had a purple glass visor covering her face. Only her white eyes were visible and they looked directly at the new comers.

"What's going on Wrex, who are these people?" she asked, fear in her voice.

"Don't worry, they are here to help get you someplace safe." Wrex said gently as Jack walked up to her, extending his hand.

"I'm Commander Jack Darby and this is Lt. Cmdr Kaiden Alenko of the Alliance, we are here to take you into protective custody miss.."

She looked at both men for a moment.

"Tali….. Tali'Zorah nar Raya" she replied as she took his hand and stood up. Jack then turned to Wrex and Garrus.

"Is there a faster way out of here than the way we came in. I don't think that would good idea to go back, especially if the men that are after Miss Raya here are still out there?" he reasoned. The Quarian looked at Jack.

"Please call me Tali" she insisted, Jack smiled back in return. "Ok Tali" he said gently before returning to the others. "So is there another way out of here?"

Garrus shrugged and Wrex rolled his eyes at the Turian in amazement before walking over to the back wall and pushing against it. Causing it to open up revealing a hidden exit.

"I noticed that this was here the last time I stayed, obviously the new owners never figured it out."

Jack smirked as he offered Tali his hand, which she gratefully took and lead her through the hidden exit onto a balcony outside. Kaiden saw a mechanised ladder and activated it, making it extend all the way to the ground. Kaiden then climbed down first followed by Garrus, then Tali and finally Jack and Wrex. They then started to head away from the club when armed Batarians and Humans appeared out of the shadows and surrounded them. They were wearing the white and blue armour of the Blue suns mercenary group. Jack and the others equipped their own weapons and stood in a circle with Tali in the middle, out of view of the newcomers.

"Give us the Quarian and you can walk away." the lead Batarian offered dryly as he signalled his men to walk closer to the group, weapons armed.

"Why, who hired you to take her out?" Jack asked not taking his aim off the leader.

"That's none of your concern alliance scum. We have been tracking you since you entered the under city, we knew that you would lead us directly to the girl. Now hand her over to us, or this will end bloody for you."

Jack glanced over to Garrus who was holding what looked like a grenade in his right hand and nodded slightly.

"That sounds like a good deal, but I have a better one. How about you let us pass and you don't leave the Citadel in body bags" Jack answered cooly.

The leader gritted his teeth as he lost his cool and yelled at his men to fire at them.

"Garrus now" Jack ordered as the Turian threw the grenade into the air where it exploded bathing the entire area in a white light.

Before the light had a chance to fade, Jack and the others killed the mercs before they had a chance to recover, leaving only the leader left standing. Once he had recovered his sight he looked around to see his men scattered around on the floor before his eyes landed on Jack standing in front of him, gun pointed at his face.

"Now how about we make a new deal, where you get to keep your life?" he asked calmy, his face remaining stoic. But to his surprise the leader chuckled which completely threw Jack off.

"What's so funny?" Kaiden asked stepping forward.

The leader looked up to the balcony and smiled, making the group look up too to see three more mercs standing over them, guns trained on the group. The leader then loosened up and held out his hand.

"Give me the gun?" he said to Jack as several more mercs appeared around them. "And the rest of you drop your weapons, I want ask again."

Jack looked back at the others and nodded. Each one dropped their pistols as Tali looked around panicking.

"Oh keelah" she said under her breath.

"You didn't think that I wouldn't have back up did you?" the leader gloated at Jack as he walked forward towards Tali. Jack glanced over to the new men on the ground with them. They were not carrying firearms like the others earlier or the ones now on the Balcony. They were only armed with combat knives. He looked over to Garrus and Wrex who looked back at him like they were all on the same page. _'If there was only a way to take out the gunmen on the balcony then these guys would be no trouble'_ he thought to himself as the leader grabbed Tali by the arm and dragged her away from Jack and his friends.

"It was nice doing business with you" the leader gloated as walked past Jack with Tali.

"Kill them!" he ordered to his men as Tali tried to break free of his grip.

"NO!" she screamed as she anticipated the mercs gunshots. But after a moment nothing came.

The leader suddenly looking irritated looked up towards the balcony as did Jack and the others. What they saw was not three gun men looking down at them, but a blue haired young woman standing amongst the now unconscious mercs that littered the balcony.

Jack smiled as his eyes met the woman's electric blue ones.

"Hi Jack, I'm not interrupting anything am I?" she asked with a smirk on her face.

"Not at all, how about you wait right there, while we throw out this trash?" he replied as the leader just looked at both of them, utterly confused. The blue haired woman then folded her arms and lent forward on the balcony's rail.

"Don't know, I might get bored before then? She said acting coy. Jack chuckled at her response. "We wouldn't want that now would we?" he answered. It was funny, he hadn't seen her for years and he had thought that their first meeting would have been awkward. Yet here they were, talking like nothing had happened. He had missed that.

"What the fucking hell is going on here?" the confused Leader screamed regaining Jack's attention.

"Well this is what is happening." Jack responded by punching the Batarian squarely in the face, knocking him to the ground. Now free, Tali ran to the side to get out of the fight as Jack and his friends and the mercs suddenly turned the area in to a street fight. Garrus kicked one merc in the stomach before pushing him into the nearest wall. Wrex grabbed two mercs with both hands and slammed them into each other. Kaiden threw punches at one merc while Jack had turned his attention to two mercs who charged at him. One swung a knife at Jack, who caught the man's attack in his hands and twisted his arm, the sudden pain causing the merc to drop the knife. Jack then kicked at the guy's kneecap, forcing him to the ground as the other man came in from behind. But the Commander spotted him and hit in the face with a back kick, sending the merc flying backwards onto the floor.

Arcee just relaxed and leant against the rail watching Jack take out one merc after the other. Sure the other guys with Jack were good fighters, the Krogan was devastating, but she liked watching Jack. He had become an excellent fighter since the last time she saw him years ago. Back then what fighting skills he knew was from watching martial art films with her back at the silo, or in the garage of his mom's home in Jasper. When June had gone to work at the hospital on a night shift, he would bring out the TV and sit and with her and watch Bruce Lee movies.

She then chuckled when Jack threw one of the mercs into the nearby wall like a rag doll. But her happy mood suddenly changed when unbeknownst to Jack, the Leader had gotten up and was charging at him with a knife.

Jack had just taken out the last merc when he saw Garrus point and shout at him.

"Jack behind you!"

Hearing this the Commander spun around to see the Leader with the knife mere centimetres from his face. But he did not move any further and Jack looked behind the Blue Sun commander to see Arcee with her pistol, holding it at the back of the Batarian's head.

"You so much as move against my partner and I will send you to the pit you piece of scrap" she said, gritting her teeth. The leader dropped the knife and got down on his knees.

"I surrender, don't kill me, I was only doing my job." he pleaded as Jack picked up the knife and threw it away before looking at his partner with a warm smile. Her cold look softening as she looked back at him, returning the smile.

"Saved your ass again partner" she said jokingly, not moving the gun from the back of the Batarian's head.

"Hey, I had everything under control" he joked back, earning a chuckle from the femme.

Garrus and Wrex stepped in and escorted the leader away as Kaiden went over to help Tali, leaving the two partners alone. With nothing between them Jack walked over to his partner and wrapped his arms around her, embracing her. Her smile went even bigger as she returned the embrace. For the first time in years the two of them were back together and she finally felt like herself again. She rested her head against his.

"I've missed you!" she said as she gently squeezed him a little more, as if making sure that he was real. Jack felt his heart skip a beat at the sensation of what she just did.

"I missed you too Arcee." Jack replied, unable to register what was going on around them. As far as long overdue reunions go this was much better than he had envisioned. But the moment didn't last as the two of them were brought out of it by Garrus.

"Hey, I don't mean to intrude on this happy moment, but could we like get out of here before anyone else tries to take us all out."

Both Jack and Arcee suddenly looked embarrassed as they jumped away from each other, their faces a shade redder than normal.

"Yeah good idea" Jack replied as the femme tried to look anywhere but at the Turian who was glaring at both of them.

"I have a cab waiting for me at the other side of the street" She answered finally finding her voice.

"Good" Jack replied, composing himself. "Kaiden help Tali to the Cab, Garrus and Wrex watch our prisoner."

The others nodded and walked in the direction that Arcee had pointed them in. When they were again alone, they both started walking to the same destination side by side. Jack looked over at Arcee, the warm smile of his returning.

"Its really good to see you again Arcee." he said gently. She smiled warmly back, her electric blue eyes meeting his.

"Yeah Jack, its really good to see you too."

**A/N: Well I hoped you enjoyed that, please let me know what you thought of this chapter with reviews or PM's and thanks again for reading.** **In the next chapter Tali gives the Council her evidence and Jack gains another promotion.**


	5. Chapter 5

**A/N: Here is the next chapter, enjoy!**

**PRIME EFFECT**

**CHAPTER V**

The Batarian merc leader sat at table in a dark room, he had been in there for the last forty minutes and was now getting frustrated, his four eyes starting to show desperation as he frantically looked around.

"I want out, you hear me, I want out" he screamed, when suddenly the door in front of him opened filling the room with light. He closed his eyes as it almost blinded him, not noticing two figures entering the room before the door closed, blanketing the room in darkness again. The prisoner opened his eyes and looked around the room again.

"Who's there, I know someone is there, I'll tell you anything you want if you let me out."

No one answered and he felt alone.

"Well isn't that interesting" a voice suddenly said from the corner of the room. "Wouldn't you say Wrex?"

"Sure is, I never thought Blue Suns were so chatty" another voice said from the opposite corner behind the Batarian.

A small light activated above the table, illuminating it in front of the prisoner. Then the face of a Krogan entered the light.

"So are you gonna talk or do I have to crack you open." Wrex said with a fierce look. Garrus appeared next to him and placed a hand on his shoulder.

"I think you should listen to him, because I don't think that I could hold him back even if wanted to." Garrus then moved closer to the Batarian, right up to his face.

"And just so you know, I really don't want too." He smiled.

The Leader suddenly felt his nether regions get very wet as Wrex moved round the table, getting closer to him.

Meanwhile Jack, Arcee and Kaiden were with Tali. They were sitting at the Apollo café in the presidium commons. Tali was looking up at the projection of a blue sky with few clouds that was on the ceiling that ran the length of the Presidum ring of the Citadel. Jack and Arcee sat at one end of the table with Kaiden and Tali at the other.

"Quite a view isn't" Jack asked as Tali finally looked back. "It really is, I never thought I would be able to see the presidium." she replied before her eyes started to look sad as she placed her hands on the table. "Quarians have never really been welcome on the Citadel." Jack reached out and placed his hand on hers . "As long as your with us no one will give you any trouble, I promise." Tali looked up at Jack before looking around to Kaiden and Arcee who smiled at her reassuringly. She sighed and regained her composure. "Thank you Commander. Apart from Wrex, you and your friends are the only people to show me any kindness here."

"So can you tell us how you came to be caught up in all this?" the Commander asked. Tali looked away for a second as a cab flew past the café before looking back to the group.

"Well I was on my pilgrimage, when I began hearing reports of Geth activity outside the Perseus Veil which had to be impossible, since the Geth had never left our home system since driving my people out three hundred years ago."

"So what did you do?" Kaiden asked as the three of them listened to the young Quarian.

"Well I thought that they may have been making attempts to find our Flotilla, so I went looking for them. I managed to find a patrol on an uncharted planet and kill them."

Kaiden looked at her confused.

"Wait, but if you could fight then why didn't you help us out against the mercs earlier?"

The Quarian just looked at him, before tapping her stomach.

"I was recovering from an injury if you remember and I was running a fever due to the suit breach. And anyway you haven't seen me with a shotgun" she said acting coy.

"Anyway" Jack said, jumping in. "What happened then?"

" I then removed the data core from the lead Geth and hacked its files, to see if they had discovered the Flotilla's location. But what I found was something completely different."

Jack's interest peaked. "What did you find?"

Tali shook her head and crossed her arms.

"Sorry, I will not reveal it here, not until we are in front of the council."

Jack leaned back and looked over at Arcee who gently smiled back at him. He returned the smile and looked back to Tali and Kaiden.

"Well we shouldn't have to wait much longer. We gave Optimus and Anderson the heads up the moment we got back and I believe they are talking to the Council right now."

Arcee then tapped Jack's shoulder and pointed over to the right. He looked in the general direction and saw Garrus and Wrex walking towards them.

"How did it go?" Kaiden asked.

"Well there was some sweat and other bodily fluid involved that I'm trying to forget" the Turian remarked irritably. Kaiden looked at them bemused. "Wait, did you hit him?"

"Didn't get the chance. The damn fool pissed himself before I even got to lay a finger on him, never knew the Blue suns hired such losers." Wrex answered disappointedly.

"So did you get a name of the guy who hired him?" Arcee asked entering the conversation.

Garrus grabbed a chair from an unused table and sat down next to them as Wrex walked over to the bar.

"Sure did. It was someone going by the name of Sideways, does that ring a bell with any of you?"

Arcee's eyes went wide at the mention of it. Jack noticing this placed his hand on her shoulder, not noticing that he was gently rubbing it with his thumb affectionately. This didn't go unnoticed by the femme as her spark warmed to his touch.

"You ok, you look like you saw a ghost for a second there" he asked her. She gave him a reassuring smile as he let go and picked up drink of a tray that Wrex just brought over from the bar.

"I'm fine and yes I know that name though I never met him, it was of a Decepticon that had vanished during the war. He was a double agent, playing both sides in the conflict, so neither was very acceptinging of him and so he hasn't been seen or heard of for a long time since."

Jack was going to ask more about him when another C-Sec officer approached them.

"Commander Darby, I am here to inform you that the Council have requested your presence in main Chamber."

Jack acknowledged the officer and the group got up from the table and followed him to the elevator. As Arcee walked with the group she noticed Tali looking at her.

"I'm sorry but is there something wrong?" she asked trying to sound friendly. The Quarian shook her head, looking embarrassed. "No, there's no problem. Its just that you are the first Cybertronian that I have ever met."

Arcee gave her a sympathetic look. "I realise your people don't exactly trust us". Tali again shook her head as she offered Arcee her hand.

"Well I am not among them on this, because you helped save my life down in the under city and your friends with Commander Darby, so that counts as good in my book". She replied with a smile on her face, not that Arcee could see the smile due to Tali's enviro-suit. But the femme accepted Tali's hand and they shook before joining the others in the elevator.

As Jack and the others entered the Council Chambers he saw again the four Councillors on their podium and Captain Anderson and Optimus Prime standing in the box.

"Jack" a voice called from behind the group, making them turn around to see Miko and Wheeljack joining them.

"You were called here too?" Jack asked as Miko went straight up to Arcee.

"Arcee, what are you doing here?" the Gunnery chief asked. The femme looked at the woman confused.

"Well I was in the neighbourhood and thought it was about time I visited my partner."

Miko smiled and nodded. "Yes well it has been ages since you too were last together, ever since that.." Miko was about to finish when she was cut off when Councillor Tevos spoke.

"This meeting is now in session, Commander Darby I believe that you have acquired evidence that proves our Spectre has gone and turned against us?"

Jack stepped forward next to Optimus and Captain Anderson.

"That is right madam Councillor"

He then turned and motioned Tali to join him in the box, the two older men stepping out to give them room.

"This is Tali'Zorah nar Raya, she came across the evidence while investigating why the Geth were spotted outside the Quarian system. Soon after she found herself on the run from Blue Sun mercenaries who had been hired to terminate her"

Then Sparatus decided to speak up.

"And we are supposed to believe the words of a suit rat, over Saren's own testimony."

Jack noticed Tali's white eyes flare up behind her visor.

"Listen here you stupid bosh'tet I wont.." Tali shouted at Sparatus as Jack stepped in to calm her down. "Tali don't, that won't help." He turned back to the council.

"What do you mean Saren's testimony?" he asked curiously.

Sparatus then activated his holo-tool and a giant hologram of Saren appeared in the middle of the Chamber.

"Dear Councillors I wish it was under better circumstances that I contact you but when I was informed about the ridiculous claims against myself, I decided to take matters into my own hands. You see I was nowhere near Eden Prime on the day of the attack by the Geth which of course is a terrible tragedy. But I was actually on Illium hunting down a lead on the assassin that had tried to murder my good friend Councillor Sparatus three weeks ago. I do not know where or who started this incredulous rumor, but if this Commander Jack Darby knew anything of me. Then he would come to see that it would be impossible for myself to have been a part of the events at the human colony. I serve the council and the people of our galaxy as a Spectre to my absolute fullest. I do wish to give my condolences for the lives lost on that black day at Eden Prime. My thoughts go to their loved ones and I make this pledge, that I will not stop until I find out why the Geth attacked Eden Prime and put a stop to this sudden act of aggression against our worlds. Farewell."

With that the hologram vanished as Kaiden turned to Garrus.

"What a load of bullshit right?" he whispered to the Turian who nodded in approval. Optimus and Anderson and everyone else then looked at Jack who could feel all eyes on him at that particular moment. He looked back to see Arcee giving him a warm smile of support. If he knew any better it was a look that said '_You show them who's boss!'_ and he smiled backed to her in appreciation. Sparatus deactivated his holo-tool and looked down at Jack.

"So have you really got anything against our Spectre?" he asked in a sceptical and quite insulting tone. Jack though did not let that get to him as a confident smirk appeared on his face. "Yes we do honoured Councillors". He then turned to Tali who activated her holo-tool and played an audio file for everyone in the chamber to hear.

"Have you located the next Lithonian Artefact" Saren spoke as the council chamber suddenly went silent as everyone was listening intently to the audio file that was now playing.

"Yes Saren, it is located on the planet of Eden Prime, but it has been excavated by the Humans and Autobots who have a colony situated there." an unknown voice replied.

"They are of no concern, alert the Geth forces we have to attack the planet, secure the artefact and await my arrival." Saren said as gasps could be heard among the audience that was watching from the balconies high up in the chamber.

"It will be done Saren." the unknown voice answered.

"Our search is nearly over Sideways, because once we have what we need from Eden Prime, we will be one step closer to the finding the Conduit" Saren continued.

"And one step closer to the return of the Reapers" Sideways finished.

Tali deactivated her holo-tool and looked around as the audience started talking amongst themselves. Jack looked at the councillors who looked shocked at the new development. Sparatus looked absolutely furious.

"How do we even know that this evidence is even legitimate. It could be a fake." he tried to reason weakly.

Valern was working his holo-tool when he stopped and looked towards the Turian councillor.

"The Quarian has just sent me a copy of the file and I have completed the scan of it. It is genuine and the voice sample is a one hundred percent match with Saren".

The whole room went silent again as the Sparatus looked down to the ground, obviously this news had hit him hard. Tevos decided to speak for her fellow councillor.

"As this new evidence has proved that Saren has in fact gone rogue and attacked the very people and principles that he was chosen to protect, we have no choice but to strip him of his Spectre status. We wish to offer our apologies to you and your people for any animosity that we had pointed at you."

"Thank you madam councillor, we were only here to make sure that the truth was known to all of you so that Saren could be stopped." Anderson replied as Tevos nodded in return.

"Since we are now one Spectre down, Commander Darby you have proven yourself worthy of becoming the first human Spectre to the Council, but unfortunately as your race is not part of the council then you do not qualify."

The balconies above started chattering again at the councillors comments. Optimus stepped forward.

"Madam Tevos and respected Councillors, I do have an answer to the problem if I am allowed to continue" the Prime said as his face remained stoic.

"And what is it Optimus Prime." Valern asked the Autobot leader.

"As the history records show, Cybertron was once a part of this council during our golden age many millennia ago and It was the duty of the Primes to defend the rights and freedoms of all sentient life in the galaxy. But when our civil war began and we found ourselves cut off from the rest of the rest of the galactic community. This Council saw fit to hand that duty to the Spectres and it seems that they too have now failed. So I believe that it is time for one to rise up and carry the title of Prime and protect this galaxy from whatever threat that Saren is planning to let loose on us all."

The Councillors spoke among themselves for a moment, going over what Optimus had suggested.

"And would that be you Optimus Prime?" Tevos asked. The Prime shook his head.

"I maybe a Prime and the leader of the Autobots, but my time has passed. But I do know that there is a person among us today who is ready to accept this title."

Jack suddenly felt very self conscious and gulped when the Council looked at him and then his friends.

"Of whom do you speak of?" Sparatus asked, looking among the group in front of him, not looking at Jack.

Optimus turned to Jack and motioned him forward.

"Commander Jack Darby of course." he said beaming with pride.

The Turian's jaw dropped.

"But he is not even cybertronian, how can he become a Prime?" he almost shouted.

Optimus's face went stoic as he looked at Sparatus.

"To be a Prime is to stand for and protect the values that Primus himself embodies. To lead by example and inspire those around him and forever stand vigilant against those who would seek to bring darkness over us all. Jackson Darby has proven himself worthy time and again, during the final years of our civil war and after becoming a soldier of the Alliance. He is the perfect choice to become the next Prime."

Sparatus suddenly found that his voice had deserted him after Optimus had said his piece as the other councillors nodded in agreement.

Jack meanwhile had no idea what to do and his stomach felt like it was tied up in knots, but then suddenly he began to calm down when he felt a soft hand take his and squeeze it gently in support. He turned to find Arcee standing beside him, his hand in hers. She turned to him and smiled the kind of smile that would make Jack's heart skip a beat every time he saw it.

"Its time" she spoke gently to him as she let go of his hand and watched him walk up to Optimus, the look on her face was that of the same pride that was on Optimus's at that exact moment. Jack stood beside Optimus as the council studied him from their podium.

"Commander Darby, we accept the suggestion that Optimus Prime has offered us. But do you accept the title of Prime and the responsibilities that it brings?"

Jack looked to Optimus who was looking at him in a way that Jack could only describe as a proud father, a warm smile on his face. With the silent approval that Optimus gave him. Jack turned back to the council.

"I accept it with all that I am." he answered.

"Very well, Optimus Prime we leave this in your capable hands." Tevos said as the Council stood and watched history unfold in front of them. Optimus turned to Jack and removed a chain that was around his neck and hidden under his armour. On the chain, much like the one that Jack had with the key on it, was a small pendent shaped crystal. Optimus placed the crystal in the palm of his right hand and it glowed a gentle white energy as it grew into the now recognisable matrix of leadership.

"Jack take the key to vector sigma and place it in your right hand." Optimus told him. Jack nodded and took the key from under his t-shirt and held it in his right hand as it too grew to the size that it had been the last time he had used it years ago.

"Now hold it up against the Matrix and if proven worthy of which I have no doubt, then primus will bestow upon you the title of Prime." Optimus commanded. Jack nodded and held the key next to the fabled relic. As if on cue both relics started to glow a bright white light that encompassed both Optimus and Jack and making everyone cover theirs eyes. After several seconds the light died down and everyone looked at Optimus and Jack. Optimus had no changes to his person, but the same could be said of Jack who first looked at the object in his hand. Gone was the key to Vector Sigma and it was replaced with a silver and gold relic that had a doughnut like shape with a white shining crystal in the hole at the center. Jack then noticed that he was no longer wearing the clothes that he had worn in the Undercity, but instead was wearing an armour that he had never seen before. It was dark grey and had a very sleek and lightweight design to it. It had a red stripe with thick silver outlines going down both of his arms from past the shoulder pads that ended at his gloved hands. And on right side of his chest plate where the Alliance insignia would be, was a Silver Autobot insignia with Red outline. He smiled at his new look before looking back up to Optimus.

"Primus has found you worthy Jackson Darby and has given you the Star of Terra, the Human matrix of leadership, inside it contains the wisdom of the Primes and is a sibling to the matrix that I carry. You are now Jackson Prime, the first Human Prime."

And with that the chamber filled with the sounds of applause as everyone from his friends and the audience, and even the Council were applauding the new Prime as both he and Optimus watched as their matrixes shrunk back to the pendent sized crystals for them to wear on their person.

After the applause had died down. Tevos stood forward and looked at the new Prime in front of her.

"Jackson Prime, we thank you for what you have done for us this day by showing us Saren's true self and for accepting the role of this cycle's Prime. We now order….no we ask that you stop Saren from achieving his goal of finding this Conduit. We may not believe in the Reapers as a threat but Saren and the Geth force under his control must be delt with. Will you do this for the galaxy?"

Jack took a step in front of Optimus and saluted the Council.

"I will madam Councillor. I will do everything in my power to bring Saren to justice."

Tevos smiled as did Valern and Perceptor, Sparatus though gave a nod of respect to Jack.

"Then go with the knowledge that this Council grants you every resource that you will require in you mission. Good luck to you Jackson Prime."

With that the council left the chamber as Jack was left with his family and friends smiling back at him as they grouped around him.

After leaving the Council Chamber and being congratulated by each of his friends. Jack noticed Arcee checking out his new Armour.

"I have to say that armour looks really good on you Jack." she said with a playful smile.

"Thanks," he replied shyly, his face going slighty red from all the attention he was getting or maybe it was the way Arcee had just looked at him. He wasn't entirely sure which it was.

"It doesn't even feel like I am wearing it. It's not the least bit heavy." Jack added as Optimus walked up to both of them.

"I believe that armour holds more surprises for you that will reveal themselves when needed." he said with a proud smile. "I am very proud of you Jackson, but I believe that Captain Anderson would like to speak to you."

Jack turned to Anderson who looked at him with a proud look, not the first Jack has seen in the last half hour or so.

"Commander Darby or is it Jackson Prime?" he asked a little confused.

"Jackson can use both titles, it is not one or other" Optimus told Anderson which the man nodded at in understanding.

"I have another surprise for you Jack, I will be staying aboard the Citadel when the Normandy leaves. Instead you will be the ship's commanding officer from now on. After all you will need the ship more than I will." he continued as he offered Jack his hand.

The surprise in Jack's face made both Optimus and Anderson chuckle before Jack shook Anderson's hand.

"Thank you Anderson, I will take good care of her." he replied. Jack then turned to Wrex, Garrus and Tali.

"Hey guys, you know we made quite the team earlier today. Is there any chance I can convince you to join the us on the Normandy?" he asked as he was joined by Kaiden, Miko and Wheeljack, not noticing Arcee who had slipped by to speak to Optimus in private.

"Hell why not, count me in Darby" Wrex said with a smile on his face.

"Well I don't know how much help I could be, but you did save my life back in the under city so, yes I will join you and do what I can." Tali replied.

Jack then looked at Garrus, who looked like he was thinking it over.

"Well, my father always wanted me to serve in C-Sec, but I am getting tired of all the red tape and you do seem to have a knack for finding trouble Jack so yes, count me in too." The Turain replied with a smirk. Jack shook their hands and offered them a warm smile.

"Well then welcome to the Normandy. The ship is docked at bay 23 on the presidium ring. We will be leaving as soon as everyone is ready." As the three left, Optimus and Arcee joined Jack.

"Jackson, Arcee has requested a transfer from my team to your command on the Normandy" the Autobot leader said as Jack looked to Arcee.

"I am yours if you want me partner?" she said hiding any doubt she might had had at that particular moment behind a smile. Jack looked at her and gave her a big grin as he held out his hand to her.

"I would be honoured to have my partner alongside me on this mission Arcee, if you will accept the position of my XO?" he replied gaining a shocked look from the femme.

"Are you sure?" she replied hesitantly.

"You have been Optimus's SIC for a long time Arcee, you have more experience than anyone on the Normandy, and I trust you to keep me on my toes as this is my first command."

Arcee smiled and shook Jack's hand. "Well I guess I'm your girl." she said, her face beaming.

"Yes you are Arcee." Jack replied in a gentle and warm tone that made femme's spark skip a beat.

Optimus had watched the two as they were talking and took great joy in seeing how happy they were together at this moment.

"Well it is time I was on my way. I wish you the best of luck in your mission Jackson, and Arcee take care of him."

"I will Optimus, that's a promise" the femme replied as Optimus said his goodbyes to the two of them and walked away to the transit hub. Then both partners headed for the elevator back to the Normandy.

As the Normandy left the Citadel and made its way towards the space bridge, Jack and Arcee were in the cockpit as he had just introduced his new XO to Hotrod. Both command officers were now wearing Alliance uniforms.

"Sir we are getting a data packet from the Citadel. It's the council, they have sent us information on a number of coordinates where Saren might be located, based on his past actions a Spectre as well a large data file concerning the Reapers." Hotrod told Jack as he was flying the ship.

"Thanks Hotrod, now could you patch me into the intercom." Jack asked the pilot who obliged.

"Intercom open" he replied. Jack then thought for a second on what he would say before he stood straight and started to address the rest of the ship who were listening after the intercom activated.

"Crew of the Normandy, this is Commander Darby speaking. As you know I have been given command of this ship from Captain Anderson and we have been tasked with a mission of the utmost importance. We have to find Saren before he finds the Conduit. Now I won't lie to you, this will not be an easy mission. We all saw what happened at Eden Prime and we may only be one ship. But I know that this ship and her crew are the best in the Alliance and we will not fail in our mission, because this is our chance to show the galaxy what we are capable of when we all work together. We will find Saren and put an end to him and the Geth force under his control. This I promise you all." The Commander then deactivated the intercom.

"Well said Commander and congratulations on being made a Prime. You deserve it Sir."

Jack patted Hotrod on the shoulder. "Thanks Hotrod, now take us to the first set of coordinates on the list the council sent us." Jack ordered as he and Arcee who was looking at him full of pride, turned and headed back to the CIC.

"Aye Aye Commander" Hotrod answered as the Normandy left Citadel space via the Space Bridge.

**A/N: Well I hope you enjoyed that. Again let me know what you think through reviews and PM's and thanks for reading. **

**In the next chapter The Normandy comes across a derelict starship with a terror on board beyond anything they have seen. And Jack and Arcee are forced to deal with their past.**


	6. Chapter 6

**A/N: Here is the next chapter, enjoy!**

**PRIME EFFECT**

**CHAPTER VI**

The Alliance frigate Normandy appeared from inside a plasma cloud and flew through another star system before jumping to hyperspace. It had been several days since the new Prime, Commander Jack Darby and his crew had started its search for Saren and so far the they had come up empty. They had visited several of the coordinates given to them by the Council and yet they had found nothing. What if Saren had found yet another relic of the Lithone or had discovered the Conduit already. These thoughts and more had gone through the minds of the crew as they performed their duties aboard the ship.

Miko was keeping Wheeljack company as he worked in the ship's science bay. Tali was in Engineering. Kaidan was talking to Hotrod in the cockpit. Wrex was sitting alone the Common room and felt quite bored. He activated his com link.

"Garrus its Wrex, you there you little Pyjak."

Garrus though was in the main battery room, running diagnostics on the ship's weapon systems.

"I can hear you Wrex, what's the problem?" Garrus replied not taking his attention from what he was doing.

"Are you gonna come up here and talk to me. The others are busy with whatever it is that they are doing, the rest of the crew wont speak to me." he said with a rather sad tone. "I think they are intimidated by me."

Garrus then looked up from the console. "Intimidated by a Krogan, now what would give you that impression?" Garrus replied with a chuckle.

"Yeah yeah, just get your ass up here and have a drink with me." Wrex replied with a sigh.

"Sorry, I'm still in the middle of some calibrations." the Turian replied with a sympathetic edge to his voice.

"You said that same thing two hours ago." The Krogan said bitterly as he looked down at his glass and sighed yet again as two crewmen walked in and immediately kept their distance.

Jack was in his new quarters, well they were Anderson's quarters but as he was in command now, had the honour of a more spacious room that had everything his old quarters had and a little more. It had a bathroom and also a fish tank, Jack looked over from his desk to the fish tank that was lit up in an azure blue light. '_No definitely not getting any fish for that'_ he thought to himself. The last time he had attempted to look after fish, his mother ended up flushing it down the toilet when he was younger. He turned back round to his desk and reactivated his console. There were still empty boxes lying in the corner of the room next to the far end of the fish tank, left over from his attempts of making it feel more like his own. But he had to keep on looking through the reapers file that the council had sent him before they had left Citadel space.

As he looked through the file, he could see why the Council liked to believe the Reapers were nothing more than a myth. This whole file read like one of those dark fairy tales his mother read him when he was a little kid, like Hansel and Gretel. The old witch in that one had scared him so much that he had to sleep in his mother's bed that particular night. His thoughts drifted to his mother as he recalled the conversation they had a few days ago over the stellar com. She was extremely proud of him for becoming a Prime and had faith in him to complete this secret mission that she could not know about. She had also told him not to worry about her as her husband, Jack's step father William Fowler had just bought them a new house on the coast of California and they had just moved in a few days ago. Jack had never really liked Fowler when they had first met, but they soon earned each others respect as they took part in the Autobots war. They had even grown to be friends by the end and Jack had also noticed how Folwer and his Mother had grown close. He was happy that his mother had found someone who actually cared about her compared to the other guys that had come and gone in her life. So when Folwer asked June to marry him, he first asked for Jack's consent and he gave it happily.

As Jack sat in silence he was suddenly brought out from his thoughts by a sound going off which meant that someone was waiting outside his room.

"Come in" he answered as the door opened and Arcee walked in, her electric blue eyes scanning the room before falling on Jack as he sat at his desk. A gentle smile grew on her face.

"Hey Jack, I'm not bothering you I am?" she asked as Jack returned the smile. "No not at all, actually I could use the company. This file on the Reapers is starting to give me a headache with how little it actually says on them." He replied while gently rubbing his eyes.

Arcee walked beside him and bent down placing one hand on the desk and the other on the back of his chair as she looked at the data on his screen. At this close Jack could smell the natural fragrance of her soft skin and it sent waves over him as he suddenly felt very hot. He took a deep breath before looking back at the screen. If Arcee had noticed this, she didn't show it as she continued to look at the data, but Jack couldn't see a small smile that had graced her lips.

"Maybe you could use a fresh pair of eyes on this?" she said in a gentle tone.

"That's a good idea." he replied as Arcee rose back up and walked over to get a chair. She then noticed the door to her left. Her curiosity got the better of her as the femme walked over to it and opened the door revealing a small bathroom with toilet, a sink and a fully functioning shower.

She turned to Jack with a look of surprise on her face.

"You have a shower?" she asked making Jack turn to her. "My quarters don't have one?"

Jack gave her a playful look as he looked at the femme. "Well I am the commanding officer, all the privileges and such "

She crossed her arms and tried to look as annoyed as she could though she found it hard to do with the way Jack was looking back at her.

"But you can use my shower if you like?" he said which caught her by surprise. "Really Jack?" she asked.

"Sure, we are partners after all." he said as he got up and went over to the drawer and picked out a large towel which he then handed to her. Arcee took the towel. "Thank you Jack" she smiled to him as she then turned and headed to the bathroom.

"It does only have cold water though" The Prime joked which the femme didn't find funny.

"You better be kidding because if not, then I will hunt you down…partner" she playfully replied as Jack chuckled.

Arcee then entered the bathroom only to come back out a moment later.

"There is not enough room to change in there" she observed. Jack then pointed behind him to the area on the other side of his bed. "Then get changed behind me, I promise I wont look" Jack said with a smirk gracing his face. His XO looked back at him with a look of disbelief. "Yeah sure, because you are not like other males of your species are you." she replied dryly.

" I am a Prime after all and we Primes do not lie remember" he said in kind. Arcee then motioned him to turn back to the screen, Jack faking hurt feelings as he gave her a sad smile and then carried on reading the data on the Reapers.

After a moment, making sure that Jack was true to his word, Arcee then started to undress. As he kept his eyes on the screen, not wanting to upset his partner. Jack found himself actually wanting to take a peek, but kept himself from doing so out of respect for her. When she walked back towards the bathroom she was wearing only the towel that Jack had handed her. '_Damn_' he thought, Arcee looks great no matter what she is wearing.

"I wont be long Jack" she said as she closed the door behind her. Jack then looked back at his screen only for his attention to be caught by the sound of the shower activating. He just sighed and slumped into his chair, numerous thoughts going through his mind.

Arcee removed the towel and hung it up on the wall as she walked under the shower, the warm water spraying over her. It was so soothing on her skin that she let herself completely relax. But it was at that moment that her thoughts dwelled on the man in the next room, her Jack. And she found that thinking of him warmed her spark more than the shower she was in.

After a few minutes, Arcee stepped back out with the towel wrapped around her, and her blue hair all messy from drying it with that same towel. Jack turned away again, this time without her needing to mention it. Which made her smile as Arcee got dressed, she actually thought it was quite cute that Jack had obeyed her.

"So did you enjoy the shower?" Jack ask as Arcee stepped back round to him fully dressed and her hair styled back to the way that she always had it and personally Jack loved the way she looked.

"Yes I will have to use it again" she replied. "You hungry, I was just thinking of getting a bite to eat if your interested in joining me?" she asked. Jack smiled at her and turned off his console. "Sure, feeling a little peckish myself actually, lets go see what chef has on the menu today." he replied as the both headed out of his room.

They had only got to the elevator when suddenly the intercom activated and Hotrod's voice spoke.

"Senior Officers report to the CIC, I repeat….." Jack and Arcee looked at each other for a moment and they could both see the disappointment in each others eyes as they entered the elevator.

Once in the CIC, they both walked up to the cockpit and stood next to their pilot.

"Report Hotrod, what is it?" Jack asked.

Hotrod looked up from his console at both of them.

"Commander we are picking up a strange signal coming from the star system next to one we are in. I only detected it because I recalibrated the sensors to a more sensitive calibration, so that we don't miss a thing when we entered the last system on our list."

Jack smiled at his pilot and placed his hand on his shoulder in support.

"Good work Hotrod, I think this is worth checking out"

Arcee looked at the Commander questioningly.

"Jack why do you think that?"

Jack looked over to her. "Just seems strange to pick up a signal when we are about to reach the final set of coordinates. We might have missed it if Hotrod hadn't altered the sensors."

Jack then turned back to the Autobot pilot.

"Hotrod set course for the location of that signal and engage the hyper drive."

"Aye Aye Commander" Hotrod replied.

The Normandy entered the system and flew towards a large brown/red planet with a ring of asteroids around it. Both partners were still in the cockpit with Hotrod.

"Sir the signal is coming from a star ship that is inside the planet's asteroid field. I can't get any more details from this far out."

"Then take us in closer Hotrod." Jack said. The pilot nodded and flew the ship towards the outskirts of the field and slowed the ship to a stop.

"Cant afford to get any closer with the random way that those Asteroids are moving in there. But I am getting a more clearer scan. I am also picking up an Alliance IFF code." Hotrod said while bringing up the details of the ship on his screen. The Prime and the femme looked over the details.

"Alliance cruiser Conestoga, what is it doing all the way out here in the Terminus systems." Jack asked. "How is the ship looking?"

"Sensor readings show that it has taken a bit of a beating from the asteroids but it still has about 57% hull integrity and breathable atmosphere aboard." Hotrod reported.

"What about life signs?" the Commander asked.

Hotrod shook his head in frustration. "Funny thing is whatever that signal the ship is emitting, it is blocking our sensors from detecting any life signs. But the same signal doesn't effect our sensors when it comes to anything else."

Jack mulled over what their next move would be and then activated the intercom.

"This is the Commander, Garrus, Wheeljack and Tali, I want you to meet Arcee and myself in the shuttle bay in full combat gear. And Colonel Kage, I want you and a team of marines down there ready too." Jack then motioned Arcee to follow him.

"Hotrod, the ship is yours until we return"

"Aye Aye Commander." Hotrod replied as the partners left the CIC.

Down in the Shuttle bay, Garrus, Wheeljack and Tali were waiting next to shuttle one in full armour. Wheeljack's was his usual Black and white design, while Garrus was wearing a blue and silver armour. Tali was still wearing her enviro-suit while adjusting the shotgun in her hands. Next to shuttle two was a group of marines in standard alliance battle gear. Among them was a Caucasian man in his mid forties who looked like he had seen many battles in his life.

"I cant believe that I have to take orders from that boy." he said in a gruff voice tinged with frustration.

One of the marines turned round to him, surprise on his face.

"But he is the first Human Prime sir, as well as a Commander. Surely that is enough to warrant respect Colonel?" the private asked hoping not to offend him.

He looked at the private and gritted his teeth. "Son I have spent twenty five years in the military, I have fought in some of the most dangerous conflicts on our planet. But this boy, this Jack Darby has risen through the ranks with ease, probably due to his friendship with the Autobots. I don't trust anyone who has had an easy ride, especially in our field of expertise."

One of the Marines pointed out to the Colonel that Jack had just entered the Shuttle bay. Kage looked around to see the commander in his Prime armour and walking next to him was the Autobot femme Arcee, who was wearing a blue and black armour with pink highlights on her arms and legs. Jack stood between the two groups with his XO to his left side.

"Ok everyone, the mission is simple, we are going over in two shuttles. Arcee, myself, Garrus, Tali and Wheeljack will be in shuttle one and will board the Conestoga via the bow shuttle bay. Colonel Kage, you and your team will take shuttle two and board via the aft cargo bay. Once onboard, we will search the ship and meet in the CIC at its center. Our objectives are to access the data core and find out what happened on the ship, see if the crew are still alive and assist them if possible. Any questions?"

Everyone remained quiet as Jack looked at each of them, noticing Kage's not so pleasant look, Jack walked up to him.

"Is there a problem Colonel?" The Prime asked his face remaining stoic. The colonel just stared at Jack. If this was Kage's attempt to make the Prime feel small, then he really didn't know Jack at all. "Is there something on my face Colonel?" he asked, his face remaining stoic. The two just stared at each other like statues. Neither man wanted to break first, as the room had gone so quiet that if you listened you could hear crewmen talking on the deck above. Everyone just looked at the two leaders. A slight smile appearing Arcee's face, '_that's my Jack'_ she thought as Kage finally broke the silence. "No Commander"

He didn't look happy that he had just yielded to Darby, the man he didn't believe deserved to be where he was.

"If there is nothing else…..sir" he replied in a annoyed tone.

"Carry on Colonel" Jack replied as he turned, ignoring the fact that the Kage was staring daggers into his back as he joined his team in shuttle one.

The two shuttles left the Normandy and flew into the asteroid field, dodging the huge chunks of rock that were double, some times triple the size of them. Onboard shuttle one, Jack was sitting down with Arcee to his left and Garrus to his right.

"Jack, I know you may not want to hear this, but I think Kage is going to be more trouble than he is worth." the Turian said looking at Jack with a troubled expression.

"He will do his duty, he wears the uniform." The Prime replied, causing Arcee to give her two cents. "I don't think it is that simple Jack" she said while placing a hand on his in support. Jack smiled back in appreciation. "He doesn't respect you and I can see that. Just don't turn your back on him." she said as she looked into his eyes. Jack could see the worry in her electric blue eyes.

"Ok Arcee" he then looked over to the Turian. "Garrus thanks, both of you. I will make sure not to turn my back on him." He then looked across to Wheeljack and Tali who also smiled at him in support.

"Commander we are coming up on the Conestoga." the pilot reported as Jack went over to the cockpit and looked out at the damaged ship that they were heading towards.

"Ok, land us in the in the shuttle bay at the ship's bow." Jack said before rejoining his team.

The two shuttles then split up, shuttle two went round to the aft of the large star ship as jack's shuttle flew round to the bow and into the open shuttle bay and landed.

"Sir I have established a connection to the Conestoga's systems and erected a force field and established a breathable atmosphere in the bay." the pilot said. Jack acknowledged him and opened the hatch, him and his team disembarking, weapons at the ready.

"Colonel team one is aboard, report your status." Jack said over his com link. After a few seconds Kage's voice came through. "Team two is aboard and has begun searching the ship. No sign of the crew yet."

"Roger that, we are heading towards the CIC now." Jack then closed the com as Tali activated her holo- tool and brought up a map of the ship.

"We should be able to reach the CIC via the these corridors" Tali pointed out to the group as they left the shuttle bay and promptly headed into the rest of the ship. As they walked the corridors the team found that they were almost completely dark apart from one or two lights flicking on and off every now and then.

"Well this is a good sign" Garrus said as they activated their torches and illuminated the area around them as they started down one of the corridors. Following the map that Tali had, they walked through the empty hallways but not come across one single crew member.

"Is anyone else getting a bad feeling from all of this." Wheeljack said as Arcee and their Prime took the lead.

"It certainly doesn't bode well for the crew does it." Arcee replied. "Tali, are you getting any life readings at all." the femme asked the Quarian who just shook her head.

"No, I have added my scanner to the map, but that signal is still messing with them."

Jack turned to face Tali. "Any idea where that signal is coming from?"

"No, I can't pin it down, its like the whole ship is emitting it." she answered, the confusion in her voice evident. Jack was about to say something else when Arcee froze on the spot, her weapon's torch illuminating a body lying on the ground in front of them.

"Jack, I have found something" she said with a unnerved tone. The Commander and Wheeljack walked up to investigate while Garrus watched the rear. The two kneeled down next to the body as the Autobot started scanning the body with his holo-tool. Jack looked down at it. It looked like it had been attacked by a wild animal. The flesh had been torn from the bones and the face was missing, most likely ripped off. If Arcee had been human, she would have thrown up by now. She had seen some sights during the war, but nothing like this. Jack looked at Wheeljack. "What have you got?"

The bot looked up from his holo -tool. "Well he's dead Jack" he said in a matter of fact tone. Jack looked at him with deadpan expression. "No shit, can you tell us anything else?"

"Well that whatever killed him was strong and fast, going over the marks left by the flesh being torn from the body."

Both then got up and stood over the corpse and looked back at the others. Jack saw the worry that had appeared on his team mates faces.

"This doesn't change our mission, we still have to find out what this ship was doing out here and we can only find that out at the CIC." He then activated his com link.

"Colonel Kage, we have found one of the crew dead. Have you found anything on your end."

Nothing came over the com but static. "Colonel come in" Jack said again but still nothing.

"Now that can't be good." Garrus said as he kept watch. "Maybe the signal is interrupting our com link." Jack replied before he turned to Tali.

"How far are we from the CIC?" he asked as the Quarian looked at the map. "we are not far now, just a little bit further."

Jack nodded and looked at the rest of the group.

"Ok, we're moving on, but be on your guard. Whatever killed that man is probably still here. Lets go."

The team then moved further through the ship, keeping a watchful eye on everything they saw as they tried to stay silent, so not to alert whatever could be hiding in the shadows.

When they got to the CIC, they found it the same as the rest of the ship they had gone through, empty. Wheeljack and Tali started working on the ships computers, trying to bring up whatever information they could find. Garrus kept an eye on the door they had just entered by while Arcee guarded the other, looking out into the dark corridor ahead. Jack walked over to the galaxy map that was still functioning and activated the captain's terminal. He saw the last two reports that the ship's commanding officer had recorded and played the second to last entry, keeping the volume just loud enough for the team to hear.

"_Captain's star log, 13__th__ March 2028. We have now been in this system for the past three days, while attempting to repair our engines that had been going faulty ever since we found that artefact on the planet Virmire days before. I do not know why that Spectre had ordered us to that system but I am certain that the artefact is to blame. Since we excavated it, several of my crew have complained of headaches and others have reported seeing things that are not there. Even as I record this log, I too have seen parts of the bulkheads seemingly move when in fact they did not. What is happening to us?" _

Everyone looked toward Jack.

"So this ship has been here for over a year and yet no one even noticed that it had gone missing?" Wheeljack said as he and Tali continued to work.

"And he mentioned a Spectre and an Artefact, it has to be Saren. I guess he sent this ship out here and then deleted any record of its mission." Arcee replied while looking down the dark corridor.

"And what about condition of the crew, the headaches and hallucinations they were experiencing, could the artefact be responsible. Does that mean we are in danger of falling to its effects." Tali said looking at Jack.

"I don't know Tali, but it sounded like they had been exposed to it for several days, so for the moment we should be alright. Now I will just play the last report." Jack said as he activated the terminal.

"_Captain's Star log, the date…. what was it again, It doesn't matter. I was wrong, we were all wrong. They are here to save us all, to make us one with them. Help us ascend. All we need to do is listen to their song. When I close my eyes I can see them in my mind, black shadows infesting my thoughts. I was afraid of them to start with, but not any longer. I will give my life for Sovereign…._" the captain said before the sound of something metal piercing his skin filled the room and then he was heard coughing up blood before everything went silent and the recording ended.

The whole room was quiet, as everything they had just heard sank in. Jack then turned off the terminal and walked over to Tali and Wheeljack.

"Oh keelah" Tali said as the Commander put a hand on her shoulder to reassure her.

"Have you found anything?" he asked and Wheeljack nodded.

"Yes, Saren was the Spectre in charge, he used his position to have this ship go out to the planet Virmire without giving them any additional information. Also the artefact they found wasn't Lithonian, but of unknown origin and is currently in the Science lab. I can't get anything else of any use since the rest of the database is heavily fragmented."

Arcee looked back at them. "Is it possible that the artefact is of Reaper origin?" she asked.

"It is possible, and I think it is worth a look." Jack replied as he placed his hand to his ear and activated his com link.

"Commander Darby to Colonel Kage, please come in" he said, but still nothing. Jack was about to turn if off when sound of gunfire came over the com. He then heard voices shouting, including Kage's.

"Kage come, in what's your status?" Jack asked again.

"Kage here, we are under attack by multiple enemies and have been forced to take cover in a storage room on deck 12. We have lost two of our team and could use some assistance."

Jack motioned the others in the direction of Kage's team.

"We are on our way, hang on Kage" Jack said before turning off the com and looking at his team.

"Ok, we now have a better idea of what happened here, but team two needs our help. So our new objectives are to help Kage and his team, then find this Artefact and find a way to shut down its signal so that we can communicate with shuttles, ok?"

Everyone nodded even though Jack could see that they were shaken a little by what they had just found and heard in the last few minutes. "Alright then, lets move out" he said as they left the CIC and headed in the direction that Kage's team were in.

They hadn't gotten far when a high pitch scream echoed down the corridor in front of them. They raised their weapons and illuminated the area in front of them with their torches.

"What the hell was that" Arcee asked as Jack took a step in front of her. "I guess we are about to find out what has killed this crew and who are currently attacking our other team. "Garrus said as another scream echoed behind him making him turn in its direction.

"Ok we are surrounded then, everyone take defensive positions." Jack ordered as he and Arcee kept a vigilant view on the corridor ahead of them, it was blanketed in darkness between flickers of the lights on the ceiling. Garrus, Wheeljack and Tali watched the area behind them. For a long moment all they heard was inhuman screaming getting closer from both directions. Then suddenly a horde of creatures ran out of the shadows towards the group. They appeared to be human but their eyes were devoid of life, glowing a hollow blue light as they screamed at the team.

"Fire at will" Jack shouted as they opened fire, taking down several of the creautres that were running at them, but more still came. Bullets riddling through the creaures, spilling blood all over the walls, but still they kept coming.

"They gonna be on top of us in moments Prime" Wheeljack shouted back as he and Garrus took down several more while Tali blew two others away with her shotgun.

"Take that you bosh'tet" she cried out while Jack and Arcee remained quiet and just focused on head shots, putting down a number of the enemies.

"Go for head shots and conserve ammo" Jack commanded as he took down three more that had nearly got within arms reach of them. "Start moving forward and keep this formation" he said as the group started moving while keeping the creatures at bay with their weapons fire.

"These things just don't know when to quit." Wheeljack commented as one enemy got too close, causing him to equip his sword and slice it in half, blood splattering on the wall next to him.

"Well at least they not very smart" Garrus observed as he and Tali switched positions so that she could cover him while he reloaded his weapon.

"yeah but if we let our guard down even for a second they will overwhelm us" Arcee replied as she blew open the head of one, causing its insides to hit the face of another creautre that screamed at her. Arcee then pointed her weapon at that one and fired taking its right eye out the back of its head as it then fell limp on the floor. Others running over the body as they continued to attack.

Jack then got a signal from Kage and answered it as he killed a few more creatures.

"Kage what is you situation?" he asked as he heard gunfire and inhuman screams over the com link.

"We are holding our own right now, but they just keep coming. How close are you?" he shouted over the weapon's fire.

"We are near, but have come under attack too" Jack replied as he reloaded his gun and Arcee covered him.

"We will join you in a few minutes" he said as he lifted the gun up and blew the legs from under one creature before putting a bullet between its eyes.

"Roger that" Kage replied before deactivating the com link.

They slowly made their way through the hallways while under continuous attack from the monsters. But things were starting to get desperate as they soon realised that if these things continued to attack like this they would run out of ammo before they could reach Kage and his team.

"So any ideas" Garrus asked as he took down two more with one bullet passing through both their heads.

"Nice shot" Tali said gaining a smile from the Turian. Jack took a quick scan of the corridor ahead while continuing to fire on the hordes approaching them. He then saw what looked like a gas cylinder which was on a the wall right down the bottom where the creatures were running from.

"Do you see a gas cylinder down your end of the corridor." Jack asked.

"Yeah" Garrus mentioned after spotting it. "Shoot it" the Prime replied. Garrus looked back after killing two that had gotten close. "That's your plan?"

"Yeah" Jack said with a grin growing on his face.

"Ok then, fire in the hole" he shouted as both of them shot their respective cylinders which exploded into a fireball at either end of the corridor, enveloping the horde close by and taking out the ones closing on the group. The team dived onto the floor as the fire passed over them before disappearing.

After the ringing in their ears had died down. They all got up to find charred remains lying around them and no more creatures attacking. Wheeljack looked at the bodies and smiled.

"Why didn't I think of that?" he said happily. Garrus turned to him. "Well if you had you may have brought some grenades with you." he responded with sarcasm in his voice.

"Well I didn't know we would be fighting zombies on this mission." Wheeljack answered back.

Tali looked over at one of the bodies.

"It's not a…what did you call it. A zombie?" she remarked as she took scans with her holo-tool. "They were human though but it seems that they have been heavily modified by tech. And that tech has the same energy signature as the signal covering this ship."

The others stood around her as Arcee and Jack looked at each other.

"Are you ok?" Jack asked not trying to hide the concern in his voice.

"I'm fine, just running low on ammo" Arcee replied while giving Jack a gentle smile. Jack then turned back to Tali and the others.

"Well we can figure out what these things are once we are together with Kage's team, lets keep moving."

They were about to head on when suddenly the vent covering behind Arcee smashed open and a creature grabbed her and pulled her into the vent. "JACK HELP!" she screamed as it hauled her off. Jack suddenly felt any self control he had disappear as his mind was overcome by the need to help his partner, his girl.

"ARCEE!" he yelled back as he jumped into the vent, falling down into the darkness below. While leaving his three friends alone with the sounds of more creatures screaming as they approached them again.

**A/N: I hoped you enjoyed that. Sorry that again I didn't manage to go through everything that I said I would during the notes at the end of the last chapter. But it seems that this will take at least two chapters to complete. Please let me know what you think with either reviews or PM's. And thanks again for reading.**

**Next Chapter, Jack and Arcee are alone and facing hordes of those creatures with little ammo and no way to escape. **


	7. Chapter 7

**A/N: Here is the next chapter, enjoy!**

**PRIME EFFECT**

**CHAPTER VII**

Gunfire and monstrous screams could be heard echoing down the corridors of the Conestoga as three people ran from a large horde of creatures intent on ripping them apart. They had just been separated from their friends, one had been torn away from them and into the darkness, the other went charging after her. None of them knew what had become of the two, but as of this moment they had more pressing matters like trying to stay alive.

"We got to keep moving, stay ahead of them" Garrus shouted back to the others as they kept firing back at the creatures running after them. "I'm running low on ammo over here" Tali said while Wheeljack threw her an ammo pack.

The group ran round a corner to find that they had come up to a door that would not open when Tali hit the activation panel.

"Oh now that's great" the Turian said as Wheeljack fired off another few bursts from his weapon into the crowd that was closing behind them, causing the creatures to topple over their dead buying the group several more seconds.

"Can you get that door open Tali?" Garrus asked while firing around the corner with the Autobot. The Quarian activated her holo-tool and tried to interface with door's controls. She shook her head in frustration and cursed. "its no good, I can't open it."

Garrus looked over at Wheeljack. "Do you think you can?"

The Autobot shrugged and patted Tali on the shoulder. "Let me try?" he said to her calmly as she got up and joined Garrus in keeping the horde back.

"Wait a minute, I have an idea" the Quarian said as she then worked on her holo-tool. Garrus shot down two more creatures, but the rest were closing in.

"Either of you can come up with something any time now."

Suddenly a yellow holographic ball appeared in front of Tali. "Watch this" she said happily as the ball flew round the corner and headed towards the horde who went straight for it, clawing away at it. Tali looked to Garrus. "You may want to get back here" she suggested as the Turian looked back to the ball and the growing horde surrounding it. "Right" he said as he took cover moments before the ball exploded, taking out the creatures.

"That was a drone right?" Garrus asked as Tali deactivated her holo-tool smiling back.

"Yes, I just programmed it to explode when it was too damaged to operate."

Wheeljack meanwhile hacked through the doors controls. "I got it." he exclaimed as others turned to see the doors open, all their attention on what was inside.

Jack opened his eyes to find himself lying on his front on a cold metallic floor. He slowly got up, every part of him aching. He looked around and found himself in a hallway that looked somewhat different to the ones that he and his team had explored earlier. Just how far had he fallen after he had jumped into the vent after Arcee he thought. '_Arcee_' his mind became full with images of her as guilt suddenly came over him. He should have been watching more closely, then she wouldn't have been snatched like that. '_She could be…_' no he shook his head. '_Cant think like that, she is alive. My girl is a survivor_' he thought as he looked up to see the vent opening above him. '_So where did it take you'._ He looked down and found marks on the ground that could only have been made from something or someone being dragged. He then heard a familiar inhuman scream echoing from wherever the dragging marks were leading. Now with a direction to head in, he picked up his weapon and headed down the corridor in the hope of finding his partner.

Garrus, Wheeljack and Tali all looked dumbstruck at what they saw behind the door they had just opened.

"Well you just gonna stand there, or are you gonna get in here before more of those things show up."

The three of them nodded and ran through the door to then be approached by Colonel Kage, looking worse for wear, but still alive. "Private get that door closed quickly now" he said to the young man to his side who ran over to the door and started working on it, as another marine stood watch with his weapon ready in case any more creatures showed up.

"So is this all there is, where's Darby?" Kage asked. The three of them looked down at the ground as if ashamed.

"When we were attacked, one of the creatures grabbed Arcee and hauled her into a ventilation shaft. The Commander went in after her without a second thought." Garrus reported. The Colonel just looked at him in amazement. "You telling me he deserted his team for just one of you. Why the hell did he do that." he screamed at them, making Wheeljack's eyes narrow as the Autobot found his voice and glared at the man.

"He did it because he cares about her" he answered, the anger in his voice growing. The Colonel acted oblivious to the wrecker's attitude and continued his tirade. "I don't care if she is the love of his life, a commanding officer is not supposed to leave his team just to save one life. No matter how close they are."

At this point the three of them all started getting angry at the Colonel. True this guy was an asshole that was for sure, but now he was just going over the top with his attitude towards their Commander.

"Well sir, it just so happens that she is the love of his life, it's just neither of them has actually realised it fully. And also the Commander happens to be a good friend of mine so I would suggest you keep your mouth shut the next time you want to insult him or I will show you what we Wreckers do best." the Autobot said, not even trying to hide the anger that was growing inside of him as he stood right in the Colonel's face. But before anything could happen the two marines who had just closed the door, appeared with their guns aimed at the three. The Colonel looked right in the face of Wheeljack, not the least bit impressed with the wrecker.

"I would suggest you back down, since with both Darby and Arcee MIA, that makes me the next one in charge. And unless you want to be thrown in the brig when we get back, you better back down."

Wheeljack took his hands of the hilts of his swords on his back and stood back, but never taking his eyes off the Colonel as Kage smiled back at him, revelling in his victory.

The Autobot stood back with Garrus and Tali as the two marines joined the Colonel who placed his hands behind his back.

"Now since I am now in charge, I believe that the mission should be scrubbed and we should head back to the ship before we lose anyone else."

"We cant, the Commander and Arcee are still out there and they need our help" Garrus interrupted, earning a glare from Kage.

"Yes, also the Commander's orders were clear, we have to get to the artefact and disable it so that our com links and map will function properly." Tali added. Wheeljack cocked his head and gave the Colonel an I told you so look. "I guess you didn't think of that did you?"

Kage could feel his anger at these three coming to an head, but he held it back and sighed.

"You make a good point, so we will head for the artefact and we will search for the two of them along that path, as long as you know where to look for this thing?" he asked looking at Tali.

"I have an idea about that, you see the signal looks like it is coming from the whole ship but there is a build up of energy coming from a few decks below us, here." she pointed on her holo-tool map which was still a little faulty.

"Ok, you may want to pick up some ammo packs that we have found. You will need them. Move out" the Colonel ordered as the group headed out of the room through another door and back into the ship's dark corridors.

Jack slowly followed the tracks that the creature had left, hoping not to gain any attention from the creatures that might have been in the shadows with him. He then turned a corner to find a shocking sight. The corridor had opened up into a large room filled with metal spikes that had the same creatures that had been attacking his team impaled on them. He activated his holo-tool and took some quick scans as he moved between the spikes, trying not get too close. Once he got half way through the room, he saw one creature kneeling over a body that when Jack got close enough could see was Arcee unconscious. Jack knew he had to take the creature out quietly or he would find himself overwhelmed within seconds. So he took a deep breath and placed his weapon on his back to free his hands and took one step after another as he moved up behind the creature until he was right behind it. He then grabbed the creature's head and with enough force he snapped it's neck and placed the now limp body on the floor before going to his partner's side. "Arcee…,Arcee, come on partner wake up" he said as he tried to wake her. "You really don't want to be sleeping in here".

Arcee then started to stir as she opened her eyes to see Jack looking down at her, a warm smile growing on his face.

"Jack…Jack you came for me?" she asked as he helped her to a sitting position.

"Of course I did, I wasn't going to leave my girl down here."

The femme looked at Jack in a curious way after hearing his comment.

'_Damn it Jack, great time to say what you were thinking out loud_' he mentally kicked himself, before noticing a smile appear on her face.

"I'm your girl I am?" she asked, trying to gain a reaction from the Prime who's cheeks had gone a brighter shade of red.

"Of course you're my girl, we're partners remember. Now I think we should get out of here, can you move?" he asked as Arcee got up and looked for her weapons. "I think you dropped these" Jack handed her SMG's to her. "We should be careful since neither of us has much ammo left, so I think that stealth would be the best option."

She nodded and looked around to see the spikes and their captives.

"What the scrap, was I going to end up on one those things?" she asked, fear slightly in her voice .

"I don't know but I did take some scans that we can go over once we are out of here. Lets go." he said as both of them started towards the end of the room and back into the familiar looking corridors. As Jack took the lead with Arcee watching their rear, it suddenly became clear to Jack that they were lost and that they were surrounded by possibly a hundred or so of those creatures. Jack's mood didn't go unnoticed by Arcee either who placed a reassuring hand on his shoulder.

"You ok there?" she asked in a soft tone. Jack turned to look at her when he then noticed another creature right behind her ready to pounce. "Look out!" he screamed as he instinctively pushed her out of harms way and jammed his weapon into the creature's mouth and pulled the rigger, decorating the wall with its brain. He then turned back to the femme who again looked at him in appreciation. "Thanks for the save." she said taking a breath before both of them suddenly heard the inhuman screams echoing around them and getting closer.

"Don't thank me yet" Jack replied as they both saw another horde of creatures appear just from where they came from and started running after them. "RUN?" Jack shouted as he opened fire on the group and Arcee ran ahead of him before he too turned and ran. Both gave it everything they had to stay ahead of the stampede that was following them , but the creatures were gaining. Arcee then noticed an open door not far in front.

"This way" she called back to Jack as she ran through the door and activated its controls as Jack stepped through and turned around firing a final burst of bullets at the creatures as they neared. Arcee then pressed one button and the doors slide shut with a clang of metal. Jack then noticed the hard lock lever and pulled it down making a heavy metal sound.

"That should keep them out" Jack said as Arcee looked around, noticing that the room only had one exit. "Yeah but we are trapped." She said in an almost fearful tone as she looked over to Jack and noticed something on his face. She got closer and saw a trickle of blood on his forehead. "Your hurt" she pointed out to him. Which made him put his hand to his forehead and then view it, seeing the blood on his fingers.

"Yeah, I must cut my head in the vent when I jumped in after you." he theorised as she directed him to sit down against the wall so she could treat his wound. He didn't want to, but she forced the issue by placing her hands on his arms and physically directing him to sit. He sighed in defeat as he sat down, she bent down in front of him and picked out some medi-gel from her pouch and sprayed it on the cut, causing Jack to hiss in pain. "Don't be a baby" she chuckled as he looked into her electric blue eyes.

"Thanks." he said as she cleaned his wound.

"Don't mention it" she replied with a smile. "Thanks for rescuing me back there".

Then for a moment there was a comfortable silence between the two of them as they just looked at each other. Then a loud bang against the doors shattered the moment, causing them both to look in its direction. Then another bang, and another.

"Sounds like they are trying to get in" Arcee said as she picked up her guns and checked their ammo, which made her curse under her breath. "I only have a few bullets left"

Jack lifted his avenger rifle up and pointed at the zero counter on it. "You still have more than I do".

The banging at the door continued at a steady pace, as what must have been scores of the creatures were at the other side trying to get in.

"How long do you think those doors will last?" Arcee asked, trying not to sound too worried.

"The doors looked quite strong, but depending how many of those things are on the other side, I would say not long." he replied. Arcee then turned to see a look on Jack's face that was too familiar. It was the same look that he had that night years ago. "Jack what's wrong?" she asked. Jack looked at her then back to the door. '_I cant believe that this is going to be it, that we are trapped with our backs to the wall while god knows how many of those things are just waiting to break in here and slaughter us.'_ he thought to himself as a soft finger then touched his chin and brought his eyes to the femme looking back at him, her electric blue eyes questioning. Arcee could see that something was burdening her partner like a heavy weight on his shoulders. "Jack tell me what's wrong, talk to me". She asked in a calm but almost pleading tone never taking her eyes off the Prime. Jack looked at her before sighing and looking down at the floor in defeat.

"Arcee I am sorry." he replied, his voice soft and nervous.

"Sorry for what?"

Jack looked like he was about to open up when he suddenly looked away.

"Nothing forget it." he closed off. Arcee suddenly felt anger build up in her spark.

"No, you cant do that. Your not pushing me away again." she said as she got up into a kneeling position in front of Jack and stared at him, her eyes now looked determined. The Commander looked back at her, looking like he just wanted to be swallowed up by the ground so long as he didn't have to continue this conversation. "Why what good will it do now?"

"Jack you have been holding back from me ever since we have been back together, you don't want to admit it, but I have seen it whenever we get too close, you suddenly look guilty, even if it is just for a moment." she replied her voice almost breaking with emotion. "If this is going to be our final moments, I don't want there to be anything between us, I care about you too much."

As Jack looked back into her eyes, feeling like his soul would get lost in them if he stared into them for to long, he was suddenly bombarded with memories of that night years ago.

_The war had ended only a few weeks ago, Megatron was dead and the Decepticons had surrendered. But due to the their energon supply having run out because of the conflict, the cybertronians had decided that the only way to survive as a species was to transfer their sparks to the con's pretender protoforms. In essence they would become human if only in appearance. _

_Team Prime had been the first to volunteer for the procedure, making sure that it was safe enough for the rest of the transformers. Jack was standing in the science lab at the Silo. He stood by and watched nervously as his partner Arcee was lying on a berth, next to her was a small almost featureless body of a Pretender lying on a similar berth with a sheet covering it from its chest to its feet and connected to the femme via a large transparent cable that had been plugged directly into her spark chamber. _

_Jack had never felt so nervous in his life, sure the process had worked for Bumblebee, Ratchet and Optimus who were watching with him. But this was his partner who was going through the procedure now and he was silently praying for it to work, hoping that nothing would go wrong. Knockout and Wheeljack worked the controls of the machine that was hooked up to the femme and her new body in waiting as Jack walked up to Arcee and placed his hand in hers, which made her look down at him with a smile._

"_Don't worry Jack, I'll be back before you know it." she said to him in a confident tone. Jack's face lightened up a little. "It better, because I have my new motorcycle and I would hate to have to ride it alone." he replied with a chuckle, hoping to hide the nervous feeling he had in his stomach. "She cocked her head at the comment and smirked. "Well we cant have that now can we. Besides, it will be interesting to ride a motorcycle and not be the motorcycle." she commented as Wheeljack walked up beside her and motioned Jack away._

"_Ok kids, we are ready for the transfer."_

_Jack walked back to the others, while not taking his eyes off the femme, who winked at him._

"_See you in a minute Jack" she said as Wheeljack then placed her body into stasis, making her optics close and her face go peaceful. The Autobot then walked over to Knockout and patted his shoulder, who then turned and knocked his hand away._

"_Careful, I just had this polished." the former Con responded, gaining a glare from the Wrecker. "Hey you can preen yourself all you want once you are in your own pretender body, but as of this…."_

"_Enough" Optimus raised his voice making both transformers turn and look down at the man standing in front of them. Even though he was now only a human in appearance, the Prime still had the presence of the Autobot leader that had towered over them before. "Start the procedure"_

_Feeling a little embarrassed, both turned back to the controls and activated the machine which started to hum loudly as the cable on Arcee's unconscious body started to come to life. Suddenly her body jolted which made Jack wince a little as a bright white ball of energy appeared in the cable and slowly moved along to the other end which was connected to an adapter that was in place right over the pretender's empty spark chamber. After what felt like hours to Jack but really was only a few seconds, the spark of his partner entered the body and almost immediately the body started to change. It's skin went from silver grey to pale pink as it took on a more athletic figure and it shrunk slightly to about five foot in height. The head started to sprout blue hair that also had pink highlights in it. Jack watched in amazement as its' face slowly moulded itself into what he could only describe as a sleeping beauty as it lied there motionless. Once the transfer had finished, The new human looking Arcee opened her eyes and revealed them to be a beautiful electric blue as they looked around the around the room before they stopped at the young man in front of her, holding her hand._

"_Hi" she said softly as Jack held her hand, it felt so soft in his own. "Hi" he replied smiling. "So I guess that ride is still on" he continued as she returned the smile._

_A few hours later and both Jack and Arcee were at their favourite spot atop a cliff side overlooking the Nevada landscape as the Sun began its decent below the horizon, the sky now taking on a vanilla like look. They had an incident free ride on his motorcycle moments earlier as both seemed to enjoy the silence between them as the newly human autobot sat behind Jack, resting her chin on his back and tightly holding his waist. Jack had never felt so good as his partner leaned on him. _

_But as he sat there now on the cliff with her beside him and watched the sunset before them, he found he could not keep his eyes off her. She was the most beautiful looking woman he had ever seen. She was wearing black jeans and a blue tank top that showed off her athletic figure perfectly, her blue hair gently moving in the evening breeze. _

_While it was true that over the years he had known her, he had come to find her cybertronian body attractive, it had been her personality that had attracted him the most. But he knew any kind of relationship with her would not be possible with things the way they were. _

_Now though, she was just like him, and he found that he wanted to find out._

"_It's beautiful isn't it" she said, breaking the comfortable silence and bringing Jack's attention to her fully. "Yes it is beautiful" he said looking directly at her. Having noticed this, the femme looked over at him with smirk as her cheeks went slightly red. "I mean the sunset smooth operator" she replied, her blue eyes looking at him. _

_At that moment the two of them just looked into each others eyes and Jack without even realising it, had found himself leaning closer to Arcee, their faces almost touching when his lips suddenly pressed against her own. Arcee looked shocked, but that quickly faded as she leaned forward into the kiss. For one long moment, time seemed to stand still between the two of them as they held the kiss. Then suddenly Jack pulled away instinctively as a million thoughts ran through his mind as to why they shouldn't have done it. Arcee looked at him confused. "Jack what is it?" she pleaded as he got up and looked down at her like he had just seen a ghost. "Sorry, I shouldn't have done that" he said, his voice breaking as he mounted the motorcycle, but the femme got up and walked up to him looking more confused._

"_Jack, did I do something wrong?" she quizzed him as he revved the engine, before looking at her one last time. "I'm sorry, I cant…" he trailed off as he rode the bike off into the distance leaving Arcee standing there completely lost. _

_Jack rode for what felt like hours as he replayed the events that had transpired between himself and Arcee in his mind before entering the Silo and parking up. He was physically shaking from what had happened. But he had to speak to Arcee so he walked up to her room. When he got there he saw the door was slightly ajar and looked in to find Arcee sitting against her bed with her knees up to her chest and arms wrapped around them, her face a mixture of emotions as she looked so lost and hurt. His heart felt like it had stopped at that very moment. 'God what have I done'? he thought to himself as guilt and shame took hold of him. He then turned away and walked slowly back to the main control room. _

_He had hurt her, the one thing that he promised himself he would never do to her. She had lost both her partners before Jack had turned up but he was the first partner to actually hurt her. He couldn't be around her anymore, he felt that if he was to see her every day that he would only remind them both of what had happened between them on that cliff before he ran off on his bike, and he could not bare hurting her anymore. _

_He found himself outside Optimus's room. He knocked the door twice. _

"_Come in" came the voice of the Prime. When Jack entered the room he found the Autobot Leader sitting at his now human sized desk, looking at the boy with a questioning look. "Can I help you Jackson?" _

_Jack tried to hide the shame he felt before he spoke, knowing fully well that Optimus would see right through it. He only hoped that the Autobot would not press the issue._

"_Optimus, I was wondering if your suggestion was still on offer?_"

As the memory faded, Jack found himself in the dark room with Arcee kneeling in front of him, looking at him intently. He then took a deep breath and looked directly into her eyes.

"Arcee, I am sorry for hurting you all those years ago, when I left you on the Cliffside after kissing you."

Arcee felt her expression soften. "Why did you do that Jack, did I do something wrong?"

Jack felt his hands start to shake. "No Arcee, it was my fault. When I kissed you it felt indescribably perfect. But suddenly I felt guilty?"

"Guilty?" she repeated.

"Yes" he said looking down, not wanting to see her face as he spoke. "I felt that I was forcing you to choose?"

Arcee kept her eyes on Jack, taking in every word that he said. "What do you mean, choose?" she asked.

"I know you loved Cliffjumper. Over the years I have noticed the amount of times you visited his grave atop of the silo. And I thought that by kissing you, that you would feel that we were somehow disrespecting his memory and I choked. Almost immediately after I left I felt guilty about leaving you there so I went back only to find you gone."

"Ratchet bridged me back" Arcee answered gently.

"Well I went back to the Silo and came to your room and that's when I saw you, sitting against your bed looking lost. I could see the hurt in your eyes and I decided that I wouldn't hurt you anymore, so that is why I chose to leave. I felt that if I was to stay, it would only bring you more pain and I care about you too much for that to happen. I am so sorry."

When no response came from the femme, Jack looked up to see Arcee looking back at him. Then the most unexpected thing happened. Arcee leaned in closer to Jack, he could feel her sweet breath on his face and she kissed him. It only lasted a moment, but it seemed to calm him down as she slowly broke the kiss and looked at him lovingly.

"Didn't you ever think that maybe I wanted you to kiss me." she replied with a gentle smile. Jack didn't know where to look at this moment but could not take his eyes of the woman in front of him.

"Jack", her voice going serious. "I did love Cliffjumper, but he wasn't my spark mate, neither was Tailgate. But I know that neither of them would have wanted me to spend the rest of my life alone. I want to spend my life with you…..partner." she answered as a big smile graced her lips. "Now how about you kiss me again?" she said as she leaned closer to Jack.

Jack felt a smile appear on his face as he too leaned towards her face till their lips met, sending waves of euphoria over them both. The kiss was amazing, if felt like they were swapping life energy through it as he placed his hand in her hair and she placed her hands round his back and squeezed themselves closer together intensifying the kiss. Time seemed to slow to a standstill again as they embraced each other. Finally parting when their need for oxygen came about. Both panted heavily, as they looked into each others eye lovingly.

"Well I guess this changes things" she commented as Jack smiled at her. "Yeah, it does."

Arcee cocked her head. "So where do we go from here?" she asked curiously.

"Well I think we should get out of this room first." Jack answered.

"Could be kind of rough." she said playfully. Jack gently stroked her cheek. "yeah, for them!" he replied as he felt his confidence come back with a vengeance. With the woman he loved at his side, he knew that those who stood in their way would not stand a chance.

And at that moment there were a hell of a lot of those creatures on the other side of the door that was now starting to buckle.

They seperated as Arcee equipped her SMG and extended an arm blade on her free arm. She then handed Jack her other SMG. "It has about the same amount of bullets as this one. Doesn't your amour have another weapon?"

Jack took the SMG. "Thanks, and I am not sure. Let me try something."

Jack then concentrated, his thoughts focusing on another weapon. Then suddenly his holo-tool activated and then changed colour from its usual yellow to white as it reformed into a saber like blade. Arcee looked on in amazement. "That looks a lot like the star-saber."

Jack looked up from his new weapon to meet Arcee's gaze. "Well Optimus did say that this armour would have a few surprises."

Arcee smirked at Jack. "Yeah , I wonder what the rest.." she was about to finish when the doors broke open to reveal the horde of creatures in the corridor. Jack and Arcee took up defensive stances next to each other. The creatures then lunged at the two who both fired their SMG's into the crowd as the creatures charged at them. Bullets ripping through a number of the monsters before the partners went charging into the horde, blades swinging. Jack swung his blade through one creature, slicing it in half perfectly as Arcee sliced past two others before landing a kick to the face of another. The two managed to fight their way out of the room to find themselves in the corridor. They stood back to back as the horde surrounded them. Jack sliced the head off one then impaled another then hitting one more fully in the face with a reverse roundhouse kick.

"Nice." the femme observed with a smile as she ripped one apart with her arm blades.

"Thanks, anyway I was wondering what you wanted to do for our official first date?" he asked as he sliced at another one. Arcee looked over her shoulder in astonishment at the Prime's question. "Your asking me this now?" she replied before she grabbed one and threw it into the others.

"Why not, gives us something to look forward to beyond this moment, wouldn't you agree." he said as the creatures regrouped giving the partners some temporary breathing room.

"Well when you put it that way, sure" she replied as Jack noticed some lit flashlights behind the horde approaching them.

"Get down!" came a familiar voice, as Jack grabbed Arcee and pulled her to the ground on top of him. Then weapons fire blitzed the corridor as the creatures were ripped apart by a hailstorm of bullets before falling to ground around the partners who were just lying on the ground staring into each others eyes. Arcee was about kiss Jack again when that familiar voice spoke again.

"Ok you can get up now."

The Commander and his XO stood up to see Wheeljack, Garrus and Tali standing in front of them smiling back. "Glad to see you are both alright." Garrus said to them.

"Thanks, its good to see you too." Jack replied as Tali handed them both more ammo.

"Well we didn't get here alone" Wheeljack answered as he pointed over to Colonel Kage.

"Colonel, its good to your still alive" Jack said as he walked over to the soldier. As Tali and Garrus whispered something to each other while looking at Arcee who had noticed them and glared back. The Colonel looked at Jack impressed. "I am happy to see that you managed to save your XO, Commander."

Jack looked at the area around Kage. "Where's the rest of your team Colonel?"

The older man shook his head. "I lost two of them during the creatures initial attack, and then the others…." he trailed off as Garrus stood next to the Prime. "We lost Jenkins and Murdock just before we got to you guys, in the large room behind us. They were suddenly impaled by these spikes that appeared from the ground." Arcee and Jack listened as the Kage continued. "I saw my men as they lashed about on those spikes, being changed. They were becoming like those creatures. So I put them out of their misery before the change was complete." he said with remorse in his voice. Jack placed a hand on the Colonel's shoulder in support. "You did the right thing by lessening their suffering." The soldier nodded as Jack turned to the others.

"So anyway, report your status" the Prime said.

"We are were heading towards what is hopefully the Reaper Artefact, and then we came across you and Arcee."

Jack then reloaded his weapon. "Ok then, lets move…"

The group had been walking along the corridor towards what was hopefully the source of the signal. They had not come across any of the creatures for a while now, not that they were complaining about that particular fact. Wheeljack walked alongside Arcee as Jack and Garrus lead the group.

"Arcee" he said as he looked over to her. "Wheeljack" she answered in a slightly puzzled tone. "So…..you and Jack." he carried on. "What about it?" she said acting coy.

"Just.. That its about time." He replied with a smile.

"Thanks" she responded in kind.

Jack then pointed ahead to a ray of light coming out of a doorway ahead. "I think we found the lab."

They entered a large room filled with computer screens as their attention was drawn to a large black object with blue light shining out of the patterns on its surface.

"Well I guess that's the relic then, I'll take some scans" Wheeljack said as he activated his holo-tool. Jack walked over the terminal nearest to the black object and started looking through the research.

"Well the database isn't fragmented here. It seems that the object wasn't the only thing they picked up. They also brought up a number of devices that they called dragons teeth. They had found them on the planet's surface with the remains of beings who had been impaled on them." he read as Arcee and Kage stood beside him.

"We should take this with us, Tali can you download the database off this terminal." Jack asked. The Quarian walked up and used her holo-tool on the terminal. "Sure thing Jack"

As they waited for the Wrecker and the Quarian to finish up, Jack looked around. "Where's Garrus?", they all looked around the room, but could not see the Turian anywhere.

"Out here" a voice came from outside the lab. Jack, Arcee and Kage went outside to see Garrus standing next to a door.

"I have found our way out of here." he said as pressed the control panel next to it, opening the doors. "The others looked inside. "You have found a working elevator?" Jack replied.

"Please don't thank me all at once." the Turian said happily. Arcee and Jack both slapped him on the both shoulders. "Well done, so we have a way back to the shuttles, without having to face off against anymore of the former crew of this ship. So how do we destroy that object?"

Kage walked forward to Jack and opened up the backpack he was wearing. "With this, enough explosive to take out a quarter of this ship."

Jack looked down at bomb and smiled. "Impressive, so how do we….."

Suddenly a creature jumped on Kage's back and bit straight down hard into his neck, causing blood to spill out.

"KAGE!" Jack shouted as he, Arcee and Garrus stood in shock at Kage who tried to shake off the creature as it clamped down on his neck. Regaining his composure, Jack activated his energy blade and thrust it directly into the monsters' head, causing it scream out loud as it released Kage who fell to the floor with it. Jack finished off the creature as Arcee and Garrus tried to tend to the Colonel's wound which was bleeding out.

"Commander…(cough)" Kage called to Jack while coughing up blood. "You and you team should (cough) get out of here."

Jack kneeled down in front of the wounded soldier. "We are getting you out too, I'm not leaving anyone else behind." he said with a determined look. Kage attempted to smile. "I don't (cough) think I will be (cough) coming with you. I've been at this (cough) long enough to know that this is it for me."

Jack looked up at Arcee, who shook her head sadly. "I cant stop the bleeding and the medi-gel isn't helping" she replied. Jack looked back down to Kage who beckoned him closer.

"Commander, I wanted to (cough) apologise for my behaviour towards you earlier." he said trying to speak through the pain as the femme held a bandage to his neck, trying to slow the bleeding.

"Don't speak, save your strength." Jack said back to the Colonel.

"No, I was out of line. (cough) I was wrong about you. When I saw you fighting with Arcee back there, I didn't see a boy who was out of his element. I (cough) saw a Prime." he said as he offered Jack his hand. "It was an honour to serve with you Jackson Prime" he smiled, blood trickling down his chin.

Jack took the man's hand in his own. "No the honour is mine Colonel." he replied.

Kage then motioned Garrus and Jack to move him over to the door and lean him up against its frame and hand him his weapon, just as inhuman screams could be heard in the distance. Wheeljack and Tali came out of the lab after finishing their scans and equipped their weapons.

"Throw the explosives package into the lab, I will detonate it while keeping the monsters off you." Kage said as Jack picked up the package and tossed it through the door.

The screams grew louder as the team entered the elevator and looked back to the Colonel sitting against the door. Jack was about to enter when Kage called to him, getting his attention.

"You promise me that you'll will stop Saren." he said while holding the bandage to his gaping wound. Jack looked at him, his face now completely stoic.

"I promise you Colonel." he replied. Kage smiled. "Then go, get out of here." he answered back as Jack pressed control panel inside the elvator, causing the door to shut as it took them back up. Kage then saw the hordes rushing at him as he used his strength to lift his weapon and fire bursts of bullets at the creatures taking some down while the others kept moving. The colonel then dropped the bandage as the blood started to flow out and picked up the detonator. He held it up in his hand and lifted the lid over the button and prepared to press it as the hordes were almost on top of him. "Come and get me you fuckers!" he spat at them, as the creatures pounced on him.

The elevator stopped on the hanger bay deck as Jack and his team ran out and sprinted towards shuttle two, which opened it's hatch for them.

"Do you think he.." Garrus asked as suddenly the ship was rocked by a powerful explosion.

"I think that answers your question, now get on board" Jack shouted as they all boarded the shuttle, the hatch closing behind them.

"Get us out of here now and tell shuttle one to do the same." He said to the pilot who nodded and sent the message while piloting them out of the cargo bay and into open space.

As the both shuttles reunited and sped away from the Conestoga, the large star ship was rocked by explosions across its hull until it finally exploded in magnificent fashion. Sending debris in all directions. The shuttles managed to stay ahead of the shockwave and left the asteroid field and back to the waiting Normandy.

"This is the Normandy to shuttles one and two, Commander are you there." Hotrod's voice came over the com link. Jack stood beside the pilot and opened the channel. Yeah we are here Hotrod, but we lost Colonel Kage and his team."

"Sorry to hear that, I am opening the shuttle bay doors now." Hotrod replied as Jack went back to his team mates. Arcee put her hand on Jack's shoulder, gaining his attention.

"He sacrificed himself so that we could get out of there." she said gently. Jack looked at her with a sad smile. "I know, but we have to make sure his sacrifice was not for nothing. Wheeljack, Tali, I want you two to start going through everything we brought back from the Conestoga. We may have a destination, the planet Virmire but we need to be ready for whatever will be waiting there."

They both nodded as Jack looked out of the window at the planet and wondered how many more would have be sacrificed before this was over, as the shuttles entered the Normandy's open shuttle bay.

**A/N: Now that was my longest chapter yet. I hope you enjoyed it, again let me know what you thought of this with reviews or PM's. And thank you for reading.**

**Next chapter: The Normandy heads for Virmire and Jack comes face to face with Sovereign. **


	8. Chapter 8

**A/N: Here is the next chapter, enjoy!**

**PRIME EFFECT**

**CHAPTER VIII**

It had been two hours since the Normandy had left for Virmire, leaving the debris of the Conestoga behind them. Things were quiet onboard ship as everyone felt the loss of Colonel Kage. He may have been a hard case, but he did have the crew's respect. Jack had spoken to the few marines that were there and they had sworn their loyalty to him and the ship in honour of their fallen leader. Jack walked away from crew quarters and towards the common room. When inside he went straight over to the drink and food dispenser to see what chef had made. As he looked over the meals that was there he could not help but smile. '_What no organic tofu?'_ he thought to himself, then remembering most of the meals he had while living with his mom. Because of her job as a nurse, she wasn't always there to cook him a freshly made meal. But he never resented her for that. Far from it, he loved her. He knew deep down that she would have been there more if she were able but her job was important so that they could keep a roof over their heads. So most nights consisted of either microwave meals or take outs. He shivered when he suddenly remembered the burgers he had to eat at that horrendous dinner. Damn that food as horrible. It tasted like burnt leather, how could anyone want to eat that garbage. But when he joined the Alliance he then realised what great food was and from that moment he never looked back. Jack almost drifted off with the memories that he had when he noticed Wrex sitting a table alone. So Jack picked up an apple and walked over to him.

"May I join you?" Jack asked as the Krogan looked up at him.

"Jack, sure take a seat. In fact could use the company, I am Sorry about Kage. He seemed like a great soldier".

Jack's face saddened slightly, remembering what happened on the Conestoga. "Yeah he was." Jack replied as took a bite out of the apple and chewed it slowly, relishing the fresh taste of it before swallowing.

"Well I wish I had been with you, being cooped up on this ship isn't good for a Krogan." Wrex replied dryly. "You know I have yet to see Garrus in here, he is to busy with his calibrating."

Jack then looked down at his apple before looking at Wrex. "Yeah well recently that would be my fault. I asked Garrus to double check the Normandy's weapons before we reach Virmire. Just to be safe." he said as he then took another bite out of the apple. Wrex nodded while looking a little irritated by the Commander.

"But I'm here, so is there anything you want to talk about?" Jack asked trying to get Wrex's attention away from the comment earlier.

"Well Jack, while you were on the Conestoga, I received a message from Tuchanka, my home world." he said before looking down at the table, saddness on his face.

"What did it say?" Jack asked noticing the change in the Krogan.

"One of my friends there died recently." the Krogan answered.

"I'm sorry." Jack replied, not knowing what else to say. Wrex then looked back at the Commander. "What do you know of the Genophage?" he said, his voice suddenly sounding slightly angry.

"I know that it is pathogen that has afflicted the Krogan for over a thousand years. That it basically reduces the number of Krogan born so that your population stays low." Jack replied, who when seeing the look of Wrex's eyes suddenly wished he hadn't said anything.

"But did you know that it was designed and released upon us by the Decepticons." Wrex said as he saw the shock in Jack's face at that comment. "What, how?" was all that Jack could say.

"During the Cybertronian war, both sides were forced to abandon their planet Cybertron and so spread out into the galaxy looking for new sources of energon. Now my planet had a very rich supply, but unfortunately for us the Decepticons found us. Even though we were not as advanced as them, we fought hard to defend our home from those metal aggressors. So hard in fact that the one in command of that particular force. I believe you call him Starscream had his two most skilled scientists create and spread the pathogen across our planet to make us weak and more manageable so that they could use us to mine the energon for them. To do this they used our atmospheric control pillar to spread the Genophage. The pillar was built long ago by an ancient race who were there while our race was very young."

Jack listened to every word the Krogan said, before the last part got to him. "You mean the Lithone" Jack jumped in. Wrex nodded "Yes, now don't interrupt" he barked at the Commander who just looked at him with stoic expression, not giving into the Krogan glaring at him. After Wrex calmed a little he continued.

"Now my father told me this next part, since he saw it while he was a child. But on that day at the pillar, he saw both of the scientists. One was purple and slightly bulky, with a large gun for an arm and had one red optic, while the other was of a sleek design, dark blue and his face was covered by a visor. Those are the two who started the darkest chapter in my race's history and when I find them, in what ever form they now inhabit. I will make them pay for it in their blood." Wrex finished as he then noticed Jack looking away for a moment.

Jack knew who both of the scientist cons were, but he didn't know if Wrex should be made aware of it at this very moment, not with a big mission ahead of them.

"Jack, what is it? The Krogan asked noticing the change in Jack's behaviour.

"Well its just that I know who they are, their names are Shockwave and Soundwave. I have seen them both during the last years of the war on Earth." Jack answered and then waited for the inevitable rage from the Krogan. But it didn't come, instead Wrex smiled at Jack. "Thanks for telling me Jack, I now have names to follow up on after this mission is over. Don't worry I wont let it interfere with what we have to do."

Jack smiled back at the brute. "I appreciate that Wrex." gaining a chuckle from the Krogan.

"As I do for you spending the time to listen to me, you're a good friend Jack Darby." he replied before Jack got up and left, saying that he would speak to him more later.

As Jack stood by the elevator waiting for it to open, he looked over to see his old quarters, now resident to his partner and XO. He smiled to himself as decided to go and pay her a visit. He rang the door chime and immediately heard. "Come in" as the door opened allowing him to enter. He walked in to see that Arcee had decorated the room with numerous belongings of hers and saw the femme sitting on the bed looking out of the window into the hyperspace field that was surrounding the ship as the stars sailed by. She looked over to Jack and the most beautiful smile he had ever seen graced her lips as Jack walked over and sat on the bed next to her.

"Hey, I was just thinking about you partner." she said warmly as Jack looked out of the window.

"Yeah, all good I hope?" he replied just as coy. Her smile widened and her cheeks reddened slightly as Jack turned to face her.

"Of course" she answered as she leaned closer to the Prime, he himself leaning toward her until their lips joined together for one long moment. They then parted, panting slightly. Jack looked into Arcee's eyes lovingly. "I'll never get tired of that." he said as they embraced each other in a hug. "Me neither" she replied as they kissed again, this time for longer and more passionately as they laid down on the bed. Both hoped this moment would never end, but then the intercom went off, startling the lovers.

"Jack, you there, its Wheeljack" the wrecker said over the com, earning a sigh from both of them as Jack lied on top of Arcee.

"Yes Wheeljack, I am here." he replied trying to hide the annoyed feeling he had at that very moment.

"Well, Tali and I have finished our research and would like to brief you on what we have found." WheelJack answered. Then Jack and Arcee heard another voice talking to Wheeljack in the background making him speak again. "Oh and if Arcee is with you, better bring her along too." he said. The two then frowned when they heard Miko's voice along side the Wreckers. "Of course she is with him".

Arcee muttered a curse under her breath which Jack could only guess had to do with Miko's impending doom.

"Ok we will be both up in a moment." he said as he then turned off the intercom, cutting out Miko's voice saying "See I told ya".

Jack looked down at Arcee who's face had gone from annoyed to disappointed as he brushed his hand through her hair..

"Well duty calls" he said sadly. "Rain check?"

Arcee's expression lightened as she smiled up at him. "Definitely".

They then kissed once more before they both got up off the bed and headed towards the door. Jack offering her his hand and the femme excepting it affectionately, as they left for the science lab.

As Jack and Arcee entered the science lab, they found Tali working at a console and Wheeljack standing around a large round table with a set of controls in front of him. Miko was at his side with a huge grin on her face. "I think that's fifty credits you owe me" she said in a very proud tone as she held her hand out to the wrecker who looked at her bemused. "Ok that's enough of that." Jack replied in stoic manner as his he and his partner and stood at the other side of the table, holding hands under the table out of view. Arcee gently squeezing his in appreciation. "So what have you got?" the commander asked looking at both Tali and Wheeljack while ignoring Miko's annoyed look. The Autobot composed himself before beckoning the Quarian to his side and activating the holo-emitter in the center of the table. Suddenly a bright orange and blue display of information, graphs and screens appeared in front of them.

"Well Commander, we have finished our examination of the evidence we collected on Conestoga and analysed it against the data from the Reapers file. It seems that the Reapers use ships like the one we saw at Eden Prime to destroy all organic life every hundred thousand years. Why they do that, no one knows. What else we know is that those same ships emit a field around them which can effect an organics mind and turn them against themselves and others." Wheeljack said as the images in front of them changed.

"You mean indoctrination?" Jack replied as he looked at an old drawing of people worshiping a black ship. "Exactly, I guess that explains why the crew of the Conestoga suddenly decided that to impale themselves on those spikes." Wheeljack explained as Arcee looked at the image of those spikes. "What can you tell us about those things." she asked as Tali took control of the holo-emitter and brought up a large scale model of the spikes.

"It seems that these dragon's teeth as they were nick named are used to produce Husks. That is what the scriptures in the file call those creatures we encountered on the Conestoga. The Reapers would plant these spikes on a world and by indoctrinating the population, they would have them turned into those monstrosities. And they do this by releasing nanites into the host that then convert the host's skin, organs, everything into cybernetic material. Therefore turning the host into a synthetic organic drone, ready to do what ever the Reapers want."

Jack looked over to Wheeljack. "So where does Virmire come into this?"

The Wrecker looked over to Tali and nodded as she activated another hologram, this time of a planet. "It seems that this planet is off the last set of coordinates we were given by about fifty light years." he replied as he deactivated the holo-emitter.

"So if we hadn't gone to the Conestoga, then originally we would have gone to those coordinates and probably found nothing." Jack replied to which Wheeljack nodded. Jack then activated his com link.

"Hotrod, this Commander Darby, set course for Virmire, but drop us outside its system with the steath mode online and launch a class five probe so that we can see what is waiting for us." he said as the Autobot and Quarian walked around to him.

"Yes sir, we will be at the Hoc system inside of a few hours." Hot rod answered before the com link deactivated. Jack then turned to the others. "Well I suggest you all get some rest and prepare for the mission. We will all meet in the briefing room after we receive the telemetry from the probe, dismissed."

As the others left for their quarters, Arcee looked at Jack who looked like he had a umber of thoughts going through his mind.

"Are you ok?" she asked tenderly. Jack gave her slight smile. "Yeah, its just I have a bad feeling about this."

Arcee took his hand into hers. "If you want I could stay with you until the call comes in."

Jack smile back to her. "I would like that." he replied gently. They then left the science lab and went to Jack's quarters together.

The Normandy exited hyperspace and its hull shimmered as it activated its stealth mode and slowly made its way to the outer edges of the Hoc system. Once in position it launched the probe which flew into the system towards the green and blue planet of Virmire.

As Jack and Arcee lied on his bed together, Jack was resting his head on his right arm while he held her close with his left. Arcee herself was resting her head on his chest and listening to his heart beat while fiddling with one of the buttons on his uniform. She enjoyed listening to the steady beat of the Prime's heart, as it made her feel peaceful. Neither of them had spoken in the hour or so since they had entered his quarters, words weren't needed at that moment for how they felt for each other. They were just enjoying their company, while waiting for the inevitable call to come in. Then the intercom came to life.

"Commander Darby we are receiving telemetry from the probe."

Jack and Arcee slowly rose from the bed and sighed.

"Thanks Hotrod, Arcee and I will review the findings in the science lab and then could you inform the rest of the team to meet us in the briefing room in an hour." Jack asked as he felt Arcee rest her chin on his shoulder.

"Sure thing Commander. Hotrod out."

The femme then affectionately nudged him. "lets go Commander"

Jack turned and smiled at her. "Ok, lets do this." he replied as the both got up and too the elevator to the third deck.

Garrus was the last to enter the Briefing room and take his place around the long rectangular table alongside Miko, Wheeljack, Kaidan, Wrex, Tali, Arcee and Jack who's face was as stoic as ever.

" I called you all here, because after looking at the data from the probe, it appears that we have found Saren's base. Due to the large facility on the planet's surface and the several Geth Cruisers in orbit around the planet. I am going to need everyone on this mission, which will be to infiltrate the facility, find out what Saren is planning and then destroy the base and take out Saren if he is there. We will be splitting into two teams, Alpha team which will comprise of myself, Garrus and Wrex and Kaiden. Beta team will be Tali, Wheeljack, Miko and Arcee who will be the team leader. We will be taking shuttle one own to the surface after the Normandy drops us off behind Virmire's moon and then engages the Geth ships and draws them away from the planet allowing us to enter without incident. Once there we will land a few clicks west of the target and then split up, entering the facility via multiple areas of access. Now I don't know what we will find down there, but with the number of Geth ships in orbit. Geth centurions are a definite, and possibly Husks since this is the planet where the dragon's teeth was found." he said as he looked at his team. "Any questions?"

Everyone looked around to each other before looking back at the Prime who smiled. "Ok, suit up and meet me down in the shuttle bay in twenty minutes, dismissed."

With that everyone left the room as Jack was left with his thoughts.

The Normandy had made it to the moon without incident thanks to its stealth mode and released the shuttle which waited as the frigate took up a position next to it.

"This is the Normandy, all systems ready to go." Hotrod said over the com.

"Roger that Normandy, Hotrod give them a good show." Jack replied.

"I'll do my best, Normandy out." Hotrod finished as the Normandy flew out from behind the moon and moved at top speed towards the Geth fleet. As the frigate entered weapons range, Hotrod deactivated the stealth mode and fired its javelin torpedoes which tore through the first Geth cruiser, causing explosions along its hull as the Normandy flew past and fired at the next ship, gaining the same results. Hotrod then turned the ship toward another cruiser and fired again only for the torpedoes to detonate harmlessly against the cruiser's shields. At this point the rest of the Geth ships had started to turn towards the Normandy and Hotrod pulled the ship into a one hundred and eighty degree turn, then flew back towards the enemy as it evaded the incoming fire. It fired its torpedoes at numerous targets until it flew through the fleet and back into open space, the Geth ships pursuing.

With the Geth cruisers seemingly distracted, the shuttle left the dark side of the moon and flew down to the surface of Virmire. The shuttle landed just outside the perimeter of the base which was based on the coast. Jack and the rest disembarked and immediately split up into the teams and headed off to their target areas. The journey to the facility went without incident, no Geth or Husks were encountered. Looked like the plan had gone of without a hitch, make it look like an Alliance frigate had stumble upon the Geth and make a quick attack before turning tail and running like hell. Saren obliviously didn't think that there would be a ground assault to deal with and so had not increased the guard. As they entered the facility's outer area, Jack spotted two Geth centurions and signalled the others too switch to silencer mode on their weapons. He and Garrus then took aim and killed both Geth with shots straight through their heads.

"Its funny how we haven't came up against much opposition yet Jack" Garrus said as Jack took out another Geth before turning back to the Turian. "It does seem a bit too easy doesn't it." he replied before activating his com link. "Beta team this is Darby, report status."

Arcee's voice then was heard over the com. "we have just entered the Facility grounds, have only come up against a few Geth and taken them out without alerting anyone." Jack kept his hand to his com link while Garrus, Wrex and Kaiden kept watch. "Roger that, Arcee stay safe." Jack replied as Wrex spotted a squad of five Geth walking off to the east of their position caring something that looked familiar to him.

"You too partner" Arcee finished as Wrex tapped Jack on the shoulder gaining his attention.

"Jack, I think we should go that way, those Geth I just spotted were carrying something interesting." He pointed Jack in the direction the squad headed in.

"Ok, lets see what they are up too." He replied as they moved slowly after the Geth,

Arcee and her team were on the other side of the Facility and had just taken out another Geth Squad.

"Let me take a look at the Geth leader there." Tali asked Arcee as the others watched the area around them. "If I can hack into its memory banks, then I can find out what they have been doing here." she finished. Arcee looked down at the Geth before nodding in return, making the Quarian activate her Holo- tool and scan the Geth.

"Anything interesting Tali?" Miko asked.

Tali's eyes went wide and she gasped.

"What, What is it?" Arcee asked noticing the Quarian's expression. She then looked up at the others.

"We need to get Jack out of here now!"

The Geth entered a room inside a large building as Jack and Alpha team shadowed them to the door way, the Commander and the Turian standing at the doorway looking in while Kaiden and Wrex waited beside them.

"What do you see in there?" Wrex asked as Jack and Garrus scanned the room. What they saw was a large room filled with capsules with creatures in them. They then looked at each other surprised after noticing what the creatures are.

"Can't be…there are Krogan in that room." Garrus said, then noticing the glare Jack gave him as a certain Krogan behind them suddenly became enraged.

"They have my people!" he cried out charging into the room leaving the others in his wake, as he fired his shotgun into the backs of the first two Geth. Making them fly forward into the two centurions next to them sending them tumbling. The Geth leader turned round and fired a shot which narrowly missed Wrex as he then shot the Geth in the face. He then walked straight up to the capsules and saw the sleeping Krogan within them, not noticing the two Geth that were knocked to the floor get up and raise their weapons. He heard them and turned around only to witness the Geth fall to the floor dead as Jack, Garrus and Kaidan walked in behind them.

"That was a stupid thing to do Wrex, what if they had set off the alarm." Jack ripped into him, making the Krogan stomp right over up to Jack's face. "They have my people in there, we have to get them out." he raged as jack stood his ground.

Kaidan was at the computer console and reading the data it showed.

"Hey guys, look at this."

Jack, Wrex and Garrus walked over and looked at the screen.

"What have you found Kaidan?" Jack asked as Wrex pushed him and Garrus out of the way.

"Well it seems that Saren was experimenting on these Krogan, giving them some sort of formula."

Wrex looked at the screen as he is eyes scanned the information before the froze on particular sentence, making his eyes widen.

"Saren has found a cure to the Genophage." he exclaimed. The others looked at him in surprise.

"Why would Saren want to cure the genophage?" Garrus asked as Jack looked to Wrex, only to find him gone. He turned around to see Wrex next to one of the capsules activating its release mechanism.

"Wrex wait!" Jack shouted. But it was too late, the capsule opened releasing the liquid that the Krogan was sleeping in as it dropped to the floor with a thud. Wrex picked the Krogan up and helped it stand.

"Easy brother, I have you." he said gently as the other one opened it eyes and looked at Wrex with a blank expression.

"Brother, what's wrong?" he asked confused by the Krogan's indifference with him. But then the Krogan's eyes narrowed before it let out a mighty roar and grabbed Wrex and pushed him into the wall behind him, stunning the brute. As the Krogan fell to the floor, the other turned to Jack and the others.

"I'm guessing he didn't want to be woken up?" Garrus joked half heartedly, gaining a glare from Kaidan as Jack noticed something about it before raising his weapon at it. It then roared again and charged at them, earning a burst of weapon's fire from the trio, putting it on to the floor. But it didn't die, as it started crawling towards them, a blood trail appearing beneath it as it moved closer to them. Jack sighed as he walked over to it, aimed his weapon at it's head as it looked up to him, again with the blank expression. He pulled the trigger and the body then went limp. Jack looked up to see Wrex watching in shock, having only just recovered as he leaned against the wall for support.

"I don't get it, why did it attack." he asked with a sad look on his face. Jack looked at him sympathetically. "Lets look at the research data and find out."

Kaiden looked over the data with Garrus as Jack and Wrex rejoined them.

"It appears that Saren has had the genophafe cure laced with the same nanites that we found in the husks, but these nanites have been altered to only change the Krogan's thought patterns to make them listen to him and him alone." He said as he worked the console. "Wait I have found an video file, just enabling." They all looked at the screen as a video of Saren and Sideways appeared with the two of them standing next to one of the capsules.

"So how do the experiments fare Sideways?" the Turian asked as the former con turned to him."

"Well with the information you brought from Sovereign, I have successfully created the Genophage cure and also laced it with the altered Reaper nanites."

Sideways then motioned Saren to view a video that Jack and the others couldn't see properly.

"as you can see the Krogan once given the cure become docile except when being given commands.

A smile appeared on Saren's lips. "Excellent, when I offer this cure to the Krogan population, they will take it happily and unbeknownst to them, they will willingly become a part of my growing army."

"An ingenious plan. But tell me, has Sovereign approved of it?" the former con asked curiously. Saren looked over to him. "Sovereign knows my value Sideways, since it knows everything that we do and has yet to stop us. I believe that we have its consensus to proceed." he replied as the video ended.

"Wait so the Reaper ship isn't Sovereign, does that mean that there is a Reaper on this base?" Garrus asked the others.

"I'm not sure, but the video's date was only a few hours ago which means that they are still here." Jack replied. "But I think it would be best if we destroy this base."

Garrus and Kaidan nodded in agreement. "Take out the base and we take out Saren, Sideways and this Sovereign. I like it. " Kaiden replied with a grin. Jack felt a hand grip his shoulder and turned to Wrex.

"We have to take the cure with us Jack, my people need it." he said anxiously. Jack looked the Krogan in the eyes. He knew how much Wrex wanted to cure his people but this wasn't the way to do it.

"Wrex, this isn't a real cure..." He was about continue when Wrex grabbed Jack and shoved him into the wall angrily.

"My people need this cure Jack and I will give it to them, and no one will stop me!" he declared, the anger making his eyes narrow at the Commander. Jack had his hand on his pistol, ready to use it on Wrex if necessary but then decided to use diplomacy.

"Wrex" he said in a calm tone. "You said that you didn't want to live under the iron fist of another. But if you use this cure. You will only be swapping one aggressor for another. Is that what you really want?" he finished, looking Wrex right in his eyes.

The Krogan mulled over Jack's words as Garrus and Kaidan trained their weapons on him, but then lowered them when Jack signalled them to.

"I will help you anyway I can to find a cure for your people Wrex, I promise you that. But we cant use this. You have to see that I am right?" Jack pleaded with the Krogan who after a moment or two, loosened his grip and released the Commander.

"Your right Jack, its just that my people have been barely able to live their lives due to the genophage. I guess I just thought that I had found our salvation. Forgive me?" Wrex said looking down at the ground ashamed. Jack picked up the Krogan's shotgun and hand it to Wrex. "Come on we have a mission to complete." he said with a smile. Wrex nodded and cocked the shotgun. Suddenly Jack's com link went off. "Jack..zzzzzz..you..zzzzzzz..need..zzzzzzz..to…zzzzzzz" then the signal cut off.

"Arcee I didn't get that, your signal's breaking up. Repeat your last message." he replied, but the signal was gone.

"Wonder what that was about?" Kaidan asked worryingly. Jack looked at his holo-tool map for Beta team's location. "They are about several hundred meters north west of us, I think we should meet back up."

The others nodded as they walked back out of the room.

"What about the lab and the infected Krogan?" Garrus asked.

"Well this place must have a reactor. We find it, set it overload and the place goes up with it." Jack replied while looking over to Wrex who nodded in agreement.

As they neared beta teams last location, having taken out an other few Geth patrols along the way. Jack's holo-tool suddenly beeped, causing jack to look at it's findings.

"What is it Jack?" Kaidan asked. Jack looked over the readings and his eyes widened. "It's detecting another Lithone artifact in a room close by." he answered surprised.

"Well I think this is worth a detour." Garrus said as jack once again tried to contact Arcee again, only to get static.

"Yeah lets go, my map says that they are heading to us anyway," Jack replied as the went in direction of the Lithone signal.

Arcee and the others ran as fast as the could as they tried to get to the Alpha team, taking out any Geth that appeared in the way. Having just found out that Jack was walking into a trap, all the femme could think about was making she her partner, her Jack was safe, as he killed yet another Geth that had turned a corner right into their path.

Jack and the others entered a room that was much larger than the lab they had been in earlier and saw that the Artefact was at the far end. As they walked up to it, jack could sense it as the others kept their eyes peeled for any surprises. Once he was close to it, Jack placed his hand out in front of the beacon to activate it, but nothing happened. Jack tried again ,but nothing.

"It has no power, it is dead." Jack said turning to his team.

"_**As you will soon be!"**_ a metallic voice boomed, making them look around to where it came from. Jack then looked above the beacon as a large orange hologram of the Reaper ship appeared over them.

"This can't be good" Garrus said as Kaidan stood beside Jack. "What do you think it is, a VI?"

"_**Small organic insects, you touched my mind. Yet are incapable of understanding what it is that stands before you."**_

Garrus shook his head. "I don't think that is a VI."

Jack took a step forward. "What are you?" he asked, his face remaining stoic.

"_**I am beyond your comprehension, I am the apex of evolution and the vanguard of you destruction. I am Sovereign."**_

Jack then realised the truth. "Sovereign isn't the name of the Reaper ship or a being occupying it. The ship itself is the Reaper."

"_**Reaper, a name given to us by the many species that have fallen to our will, as your cycle soon will."**_

"What do you mean cycle, what is it that you do?" Jack asked.

"_**For as long as life has gone on, we have been here. We are here at the apex of a cycle to harvest the strongest race that a cycle has to offer, while condemning the rest to oblivion. For that is how we go on as a species while maintaining our original goals."**_

"What do you mean original goals?" the Commander asked.

"_**Our goals are too complex for your small, feeble minds to comprehend. Your individuality makes you weak, while each of us is a nation, a collective of all the knowledge of the race that we have harvested."**_

"So every hundred thousand years you wipe out all advanced life in the galaxy, yet harvest the one race that you deem worthy of becoming one of you." Jack replied, feeling his blood begin to boil.

"_**Call it what you will, but know this. We have been at this for thousands of cycles and have never been stopped, and that will not change."**_

"Yes it will. It will because we will stop you." Jack answered back defiantly.

_**Your words are meaningless. You live because we allow it, and you will die because we demand it. This conversation is over, time for you to expire as all organics do."**_

With that the hologram disappeared.

"Well I think you just pissed him off Jack." Garrus said when suddenly a familiar scream echoed through the building.

"What is that noise?" Kaidan asked, noticing the look on Jack's and the Turian's face.

"Believe me, you don't want to know." Garrus replied as Husks suddenly rushed through the doorway at the group.

"Go for headshots to take them down." Jack ordered as they fired on the charging horde. Kaidan then looked up to see more Husks climbing down from the upper level around them. The creatures were flowing in from every angle. There was no way to cover all points of the attack.

"We are surrounded." Kaidan shouted back to others over the weapons fire as the husks closed in. Jack powered up his energy blade. "Prepare for some close encounters people." he said as the husks closed in on the group. "Wrex chuckled at the remark. "That's how I prefer things" he replied as he fired his shotgun into one in front of him. "Well I am not eally a fan of close quarters, but I'll improvise" Garrus said as he switched from his sniper rifle to avenger rifle.

The husks then pounced at them as Jack prepared to meet it head on only for a gunshot to go right through it, stopping it mid flight. Jack looked up to see Arcee on the upper floor smiling back at him with her SMG's drawn, with the others around her firing down at the husks.

"Thought you could use some backup" she said. Jack nodded back in appreciation before slicing the head off husk who got to close. After they mopped up the last of the Husks, both groups reunited outside the building.

"So once Tali found out that they had set a trap for you, we doubled back to help." Arcee finished explaining to Jack and his team.

"Well I am glad you showed up when you did." Jack replied.

"So you detected the Lithone artefact's power signature, but as soon as you got close to it, it died." Wheeljack said.

"Yeah sounds like a trap to me." Miko jumped in. Arcee then looked at Jack. "But that black ship is a Reaper?" she asked, the slight worry evident in her voice. Jack nodded back. "Yes, when it spoke to us, I could feel its animosity. It wanted me, it wanted us all dead and I know that it is capable of it."

Everyone looked at Jack, worry now written on their faces. Then Hotrod's voice could be heard as Jack's com link activated.

"Commander, thought you should know, that Reaper ship has entered the system is heading your way."

" Copy that Joker, tell me. Do you still have the telemetry from the probe?"

The group looked at Jack confused as he spoke to his pilot.

"Yes Prime, why?" Hotrod asked curiously.

"Can you tell us where the facility's reactor is and how far it is from us?" the Commander asked.

"It is pretty close to your position, it is on the west side of the complex, about five minutes if you run Prime." Hotrod answered quickly.

"Thanks, tell the shuttle to come meet us at the rendezvous coordinates in thirty minutes, Darby out." Jack finished before looking at his team.

"ok, we are going to split up again. Arcee, want you an beta team to go to the reactor and start an overload, and then meet up with us at the rendezvous."

"What are you going to do?" she asked.

"We are going back to the beacon and will remove it's memory core, before joining up with you." he replied.

"Tali you will switch places with Kaidan, since you are good with tech." he said gaining a nod from the Quarian.

"What about me?" Wheeljack said, feeling slightly insulted.

"Wheeljack, I need you to find a way to over load the reactor." Jack answered back. "Time is short, we have a Reaper inbound, so lets get to it." He finished as both groups split up again and made their way to their objectives.

Beta team had fought through quite a few Geth on their way to the Facility's reactor. It seemed that the base as now on full alert. Maybe Sovereign warned them, but where is Saren. These thoughts went through Arcee's mind as she and her team fought their way through the Geth and husk forces that were blocking their path.

After slicing down the last husk in front of her with her arm blades, the femme could see the reactor ahead.

"Ok, lets move" she ordered back to the others as they moved into the area, Wheeljack heading straight for the controls.

"How long do you think it will take?" the femme asked as Wheeljack activated the console.

"Give us a few minutes?" he answered back irritably.

"I'm afraid you don have that kind of time." came a voice from their left. They all looked over to see a Caucasian man wearing purple and gold armour. He was surrounded by husks and Geth.

"Sideways" Arcee called to him angrily, bringing out her SMG and arm blade.

"Arcee right? I would say it is a pleasure, and quite frankly it will be for me." he said before opening fire on the group causing them to take cover.

"Miko, I want you and Kaidan to cover Wheeljack." the femme shouted to them over the gunfire.

"What about you?" the gunnery chief replied.

"I'm taking Sideways." She answered, feeling anger grow inside her spark as she vaulted over her cover and stormed over to the former con's position shooting and slicing past Geth and Husk alike. While Miko and Kaidan gave supporting fire to Wheeljack who was trying to overload the reactor.

Arcee pounced at Sideways who dived under her attack and rolled over in to a kneeling position, his katana at the ready. She then activated her other arm blade and swung both in his direction as he lifted his katana to block her.

"You so much more pretty in person" he quipped at her with sly grin that made her even more angry as she broke the deadlock with him and attacked again. This time he dodged her and kicked her in the back, sending her to the floor. She got on her hands and knees and looke back at him. "Your not my type." she spat as se got up and launched into another set of moves as he dodged and blocked all of them. "I don't go for traitors and backstabbers."

He just kept that sly smile on his face as he stayed on the defensive.

"But where is the fun in working for one side when you can play both of them and come out on top." he answered as he grabbed her right arm and threw her over his shoulder on to the ground. As she tried to recover he stepped over her and held her down, getting close enough to whisper in her ear. She could feel his breath on her skin and it made her sick.

"Anyway do you really think Saren will let your boyfriend get the information he seeks." he whispered into her ear, making her eyes widen. '_That wasn't the trap earlier, Saren's setting his trap now…..JACK!'_ she thought as she let her anger explode as she wrapped her legs around the former Con's body and spun him so that he ended up on the ground and she was now on top. She then hit his face with as much force as she could muster, knocking him out.

"Thanks for the heads up." she replied as she got up and ran back to the reactor, leaving Sideway's sprawled on the floor unconscious.

Miko and Kaidan were taking out one Geth or Husk after another while Wheeljack was still messing with the reactor, when Arcee vaulted back over the cover and knelt beside them.

Miko saw the fear in the femme's face. "What's wrong?" she asked while still killing any enemy that came into her sights.

"Saren's real trap for Jack is about to be sprung." she replied.

"You want to go help him don't you?" the woman asked, seeing what Arcee was thinking.

"The mission comes first, I know that but…its Jack." the femme responded, not hiding the emotion in her voice. Miko was about to speak when suddenly the reactor started humming loudly as Wheeljack got up with his guns ready and exclaimed "We are done here lets go!".

But before her could do anymore, he was hit in the chest by several shots riddling his body and forcing him to the floor.

"WHEELJACK!" Miko screamed as she rushed over to the bot, Arcee too moving to his side.

Kaidan looked back for a moment an cursed under shi breath before continuing to fire on the approaching enemy forces.

"I don't think I should have done that." Wheeljack coughed as liquid spilled out of the bullet wounds in his chest. He then looked at Arcee. "The reactor is going to go off in fifteen minutes, enough time for you to get Jack and got off this rock." he finished.

"You too." Arcee answered, but the bot shook his head. "Need to stay and defend the position. The reactor could easily be turned off." the wrecker said as Arcee was torn between Jack and her friends. Miko then looked at her, her face uncharacteristically stoic.

"Arcee go get Jack, I'm staying to defend this position with Wheeljack."

Arcee didn't know what to say as Kaidan then jumped in. "I guess I am staying too." making all three look at him. "Hey, Wheeljack won't last that long and Miko, you wont be able to hold of all those enemies on your own, you need back up."

Miko looked away, she knew he was right, she composed her self and looked back to the young man who was still shooting Geth. "Ok then." she smiled gaining a smile in return. She then turned back to Arcee. "You better get moving, we will hold this position and makes sure the reactor goes off."

Arcee just nodded, not being able to think of anything to say.

"Oh and tell Jack if he doesn't beat Saren, then I will kick his ass." Miko finished before returning her attention to the enemy. Kaidan then looked at the femme.

"Arcee, you look after Jack now, and tell him I'll be watching over him." he said confidently as he smiled at her."I will Kaidan." she replied as she felt a hand tug her own, bringing her attention down to Wheeljack.

"We had a hell of a ride, didn't we Arcee?" he coughed as she held his hand. "We sure did Wheeljack. Bulkhead would be proud of both of you." she replied with a smile that caught even Miko's attention who nodded in kind before turning back to the fight. Taking one more look at the three of them, Arcee then turned and ran back towards the building where jack and his team were, leaving beta team and the reactor behind her.

Meanwhile Jack, Garrus and Wrex were waiting for Tali to retrieve the beacon's memory core. She was using her holo-tool while cursing under her breath every so often.

"I think I nearly have…. Damn you bosh'tet" she cursed as Garrus started tapping his foot on the ground. "No pressure Tali." he replied.

The Quarian glared at him, making Jack step in. "Now that's enough." he shouted as the two went quiet and carried on with what they are doing.

"Why don't you just shoot it?" Wrex questioned, making Tali's eyes roll. But then something caught Jack's attention and he looked over to the main entrance to see a number of Geth enter and another Turian among them.

"Saren!" Jack said as he aimed his pistol at the traitor.

"Commander Jack Darby or is it Jackson Prime, It doesn't matter does it. The last Prime I met was taller anyway." he retorted earning a growl from Wrex.

"By the way it's pointless to try to take the core, without power it is useless."

Jack looked at him and smirked. "Then you wont mind us taking it then if it really is that useless?" he replied. Saren walked towards Jack trying to look friendly. "I mean that I can't let you interfere with our plans."

Jack kept his gun trained on the Turian. "What plans, your helping the Reapers to wipe us all out."

Saren looked back in shock. "No, after Sovereign showed me it's power I joined it and convinced it of a better way. I am forging an alliance with the Reapers, between organics and synthetics. Working together for a better future, think of the lives it will save." he answered back confidently. Jack couldn't believe what he was hearing.

"Sounds to me like you have gotten too close to them." he replied.

"No, I have studied the effects of indoctrination, and I know of the dangers. But Sovereign will not take control of me, because I am still valuable to it with my mind intact. Now I will ask again, I have no need to kill a Prime, not if you join me?"

Jack looked backing disgust. "I will never join you." he spat back. Saren sighed and looked disappointed. "Well I did try... destroy them." he shouted as the Geth moved, guns blazing on the four of them.

"Cover Tali" Jack ordered as he charged at Saren, tackling him to the ground and repeatedly punching his face. Garrus and Wrex took up positions next to Tali, who was still not having any luck.

Meanwhile Saren grabbed the Commander by the throat and strangled him before throwing Jack off. He then got up and kicked Jack in the side making him wince in pain.

"I tried to be reasonable, thought that since you were apparently a Prime, that you would be willing to talk." he said as he kicked Jack in the side again, making him roll over on to his back in pain. The Turian was much stronger than Jack and had better fighting skills it would seem. The others were too busy with the Geth to help, so Jack was alone. Saren then picked him up by his throat and held him aloft before punching him a number of times in the stomach, making Jack cough up some blood.

"You humans can't handle much pain can you. I wonder how much it would take to kill you." Saren questioned as he then threw the Prime to the ground, before pulling out his gun and aiming it at Jack's body. He as about to pull the trigger when he suddenly looked away like he had heard something. He then kicked Jack aside and began walking off.

"Your lucky Prime, if we meet again, you will die." He finished as he left the building.

Jack tried to recover when three Geth came out of nowhere and stood over him, weapons trained on his hurt body. The others hadn't noticed with the number of Geth still attacking them. Jack looked up at the centurions and waited for the trigger to be pulled, when they suddenly dropped dead and familiar blue haired woman bent down at his side.

"Jack, by the Allspark. Are you alright?" she asked in shock as she saw his injuries before helping him up.

"I've been better." he replied. Just then Tali shouted "Eureka" as she pulled out the memory core, and Garrus and Wrex took down the last of the Geth.

"Where's your team Arcee?" Jack asked after seeing her on her own, she looked away in response. "They are defending the reactor until it blows." she said, her voice sounded uneasy, as Jack looked at her in shock. "What do you mean?" he asked.

"Wheeljack got the overload to start but not before being shot and so Miko and Kaiden decided to stay and defend the position." she replied.

"We have to go back for them." Jack said angrily, but Arcee held him. "We don't have time, the shuttle will be here in a moment and the reactor will go off in just a few minutes."

Jack looked around, trying to think of something they could do, but nothing came. He then felt the terrible realization, that they were giving their lives so that he could complete his mission and he had to respect that.

"OK, lets get back to the shuttle he said sadly as Arcee and Garrus helped him.

Back at the Reactor, Miko and Kaidan were still keeping the Geth and Husks at bay as she turned to Wheeljack. "We are really giving them hell aren't we Wheeljack." she said, but when she heard nothing she looked over to see his lifeless body slouched against the wall of the reactor. Miko then looked back at the battle around her and felt her eyes well up. But then a shuttle flew out from the other side of the facility, gaining both her's and Kaidan's attention. They both smiled as they knew their friends would be on board the shuttle and heading to safety.

The reactor behind them was humming so loudly now that they could barely hear themselves.

"It's been an honor Kaidan" she said to him while shooting some more Geth.

"Me too Miko." he replied as they continued to fight, ignoring the reactor which had started to glow brightly and the humming reached deafening levels.

Meanwhile the shuttle had left the atmosphere just as an nuclear explosion engulfed the facility, as well as the immediate area surrounding it. Jack looked out of the window back to the mushroom cloud that just appeared, he couldn't help but feel defeated. He had been beaten by Saren, and had lost two of his best friends as well as a comrade in arms. He stood there and said a silent pray for his two friends.

"_I am sorry Kadian and Miko!"_

_**A/N: I hope you enjoyed that. Please let me know what you think and thank you for reading.**_

_**Next Chapter: Jack is feeling defeated and only Arcee can get through to him. And the Normandy crew find out about the lost planet of Illos.**_


	9. Chapter 9

**A/N: Here is the next chapter, enjoy!**

**PRIME EFFECT**

**CHAPTER IX**

Jack lied on the bed in the medical bay as Dr Chakwas tended to his wounds. She had told him that he had three cracked ribs and sustained damage to his stomach from Saren kicking him while he was on the ground. He also had a damage around his neck from the Turian bastard's iron like grip. While he was there he had been visited by Wrex and Tali, even Garrus who had managed to pry himself away from the Normandy's weapon systems. But the one who had been there the longest was Arcee. She just sat there beside him and held his hand in support, to show that she was there for him. Nothing was said between them, as she knew Jack would only talk when he felt ready too. So she just stayed quiet and watched him as he lay there, dwelling on the recent events. But now even she had gone, and he was alone. The others had all said that it wasn't his fault with what had transpired on Virmire, but he knew different. He was the Commander, the mission leader and the one responsible for the lives of all the crew on the Normandy. But this wasn't just about losing people though, because he also had lost friends. There was Wheeljack, who though Jack wasn't as close too as he was with the rest of Team Prime was one he could still call a friend. Then there was Miko, who had been there with Jack from the very beginning. Though at the start she was irritating and hot headed, by the end she had grown into a confidant young woman with a brave heart who he was proud to call a friend, no not a friend but a sister. Then there was Kaidan who Jack had known since he joined the Alliance, he was a capable soldier and a very good friend. But now they were gone and Jack felt as if a part of himself was gone too.

The Commander had been so lost in his own thoughts that he hadn't noticed the doctor had finished.

"Commander you can get up now." she said as she looked over to him from her console. Jack sat up and swung his legs over to the side of the bed. He still felt sore, as he felt a part of his chest that was still bruised.

"Yes I repaired the damage, but the pain you are feeling should fade over the next few hours, so I suggest that you take it easy." she replied without even looking at him. Jack got off the bed and began walking to the exit. "Thanks doctor, I'll take it under advisement." he said as he left the room. Chakwas just rolled her eyes before carrying on with her work, knowing full well that he would just keep on working despite what she said.

Tali and Arcee were working on the memory core of the Lithone beacon that they recovered from Virmire. The core was actually a green crystal, about the size a baseball. Hard to imagine something so small could hold so much information. The two were so fixated on their work that they did not notice the Commander entering the lab. As Jack watched them, he could see that they were suffering from their friend's deaths too, but had buried themselves in their work to stop them from thinking about it.

"So how is it going?" Jack asked startling the two women.

"Oh keelah, don't do that." Tali bit back as Arcee gave him a slight smile. "Hey Jack, you ok?" she asked as the Commander joined them beside the crystal.

"The doctor gave me a clean bill of health" he lied hoping that Arcee couldn't see through his façade, but she just smiled at him and turned back to the crystal. Having felt like he just dodged a bullet, Jack looked over at the green rock.

"So have you guys figured out how to unlock this yet?" he asked.

"No, nothing we have is compatible with it, we have tried everything." Tali replied in an irritated manner.

"Well we have to find a way, because whatever Saren has planned, he will be executing it soon." Arcee said, her face having become stoic. She then looked at Jack and saw him just staring at the crystal. "Jack, what is it, what do you see?" she asked worryingly.

"Doesn't it look familiar?" Jack asked as he opened up his collar and pulled out the matrix crystal which then grew to its natural size in his hand. Arcee looked at the matrix and then at the Lithone crystal. "It looks an awful lot like the crystal inside the matrix." she replied as Jack picked it up in his free hand and held the two together.

"Jack be careful, we don't know what may happen." Tali warned as Jack closed his eyes and focused on what was in his hands. He then felt a strange warmth go through him, which made him open his eyes to see something he had seen before.

Jack was again standing in the ruins of the ancient Lithone city, exactly as he did before as hundreds of Reapers descended from the sky, blackening out the red hue it had. He looked around to see the bodies lying at his feet and what looked like the Lithone version of husks walking by him. They did not even acknowledge that he was there, almost like he was invisible. Then something got his attention in the sky above. He saw what appeared to be a star constellation. It's stars shining so bright that he could see them in the evening sky as the Reapers continued to rip apart the city around him with their energy beams. Jack then felt his eyes close again. When he reopened them he was back in the lab with a confused Arcee and Tali staring at him.

"Jack, you ok? You kind of zoned out on us for a moment." Arcee said with a worried expression on her face. Jack then placed the crystal back on the table and turned to leave.

"Wait Jack, your going to tell us what's going on?" Arcee pressed as she grabbed his arm, stopping him.

"I know where we have to go." He answered with a smile slowly growing on his face.

In the cockpit Jack, Arcee and Tali were standing over Hotrod as he searched through the ships star charts on his console.

"You sure you have that pattern right, because we have gone through most of the navigation data here." the pilot said as he continued to work.

"I am sure Hotrod, I saw it in a vision when I held the crystal." Jack replied.

"Maybe the crystal detected you were a Prime due to you holding the matrix at that same moment. The Lithone were similar to us Cybertronians, makes sense that they would use crystals to hold information. I wish I had thought of that earlier, but crystal storage hasn't been used since the beginning of the golden age." Arcee said with a hint of embarrassment. Jack though placed his hand on her shoulder and smiled at her. "Don't worry about it, as you said the technology was before your time." he replied encouragingly. Then a loud beep came from the pilot station. "Ok we have a match, its in the Refuge system, the planet….no it can't be." Hotrod said, his face looking shocked.

"Why, what planet is it?" Jack asked. Hotrod looked at Jack before composing himself. "It says it is the planet Ilos, but that's impossible. It is a planet that was once part of the Lithone Empire before being ravaged by what we now know was the Reapers."

Jack looked over at the console. "So that's where Saren is going then." he said.

"How do you know that Jack?" Arcee asked slightly confused by the Prime's confidence in what he just said.

"it's a feeling I have, I just know that is where Saren is going next and that we will find the conduit there as well." he said as he looked at his XO for understanding. "Do you trust me?" he said which startled her before her face relaxed and she smiled back. "Yes I trust you, partner." she replied warmly to him. Jack then turned back to Hotrod. "Set course for Ilos".

Hotrod shook his head in response. "Sir there is a problem with that. You see no one has been to Ilos in the last hundred thousand years due to a naturally occurring ion storm that surrounds the system." he replied.

"Well the Normandy is the most advanced ship in the Alliance, I think it is worth the risk if it leads us to Saren. So set course for Ilos, we will see what we can do to increase the ship's shield strength by the time we arrive." Jack ordered and the pilot nodded reluctantly as Jack joined Arcee and Tali and walked back towards the galaxy map. Arcee looked at Jack, she could tell he was still tired and needed rest.

"Jack I want you to take a few hours to rest." she said causing the Prime to look at her in shock. "Arcee, are you ordering me to my room?" he asked, the surprise evident in his face. She looked at him concerned. "Jack I spoke to doctor Chakwas and she told me that you needed rest and so she gave me the authority to relieve you, knowing well that you wouldn't do it yourself. Now we wont reach Ilos for several hours, I suggest you rest for that time." she answered, crossing her arms, her face becoming stern. Jack shrugged and admitted defeat as walked off towards the elevator.

Jack had been lying on his bed for the last few hours and he had found his thoughts drifting back to his lost friends. He didn't want to dwell, he had hoped that he could just bury himself in his work, like the others were doing. But Arcee was right, he needed to rest and so there he was. The door chimed and he acknowledged it. "Come in."

The door opened and Arcee entered his room.

"Sorry, did I wake you?" she said as she took a seat on the end of his bed. Jack sat up next to her. "No, I haven't really been able to sleep, not since.." he trailed off as he looked out of the window. Arcee looked down at the bed. She knew this was a sore spot, but she had to get him through this when they needed him the most. "I miss them too Jack, especially Miko and Wheeljack" she said, getting Jack's attention again.

"I know what you are going to say, but it was my fault and it is my burden to bear." he said, his voice cracking. Arcee got closer to Jack as she took his hand in both of hers.

"Jack, you are wrong in so many ways. Our friends chose their fate because they believed in you, in what you stand for as a Prime and as their friend." she then looked him straight in the eyes. "And so do I." she finished, her voice sounding gentle and warm. Jack didn't turn away as he stroked her cheek with his free hand, making her close hers eyes as she enjoyed his touch.

"Arcee, with everything that has happened recently, the one thing I fear the most is losing you." he said watching her eyes widen in response. "I couldn't go on if you weren't in my life." he carried on, his voice now heavy with emotion. Arcee put her arms around Jack and embraced him in a loving hug and spoke softly into his ear. "Jack you will never lose me, not now or ever, because I love you" she whispered. Jack's eyes widened at Arcee's confession as he felt her sweet breath on his ear as he then turned to face her, their faces only inches apart now. "I love you too Arcee." Jack replied as the two closed the distance and kissed while the blue/white light of the hyperspace field illuminated his room through the window. Jack then laid Arcee on the bed as he leaned down over her and kissed her again with all the passion he felt for her. She smiled against his lips as his hand trailed down to her breasts and squeezed one gently. She moaned softly while returning the same passion into their kiss, intensifying it further. Her hands grabbed his shoulders and held on as he then wrapped his arms around her and lifted her onto his lap, allowing her to straddle him. She then undid and removed his shirt before leaving a trail of kisses from his neck then down his chest. He in turn removed her top as he kissed her neck, making her shiver in his embrace. They then removed the rest of their clothing while never taking their attention away from each other as Jack then lied on top of her as she wrapped her legs around his waist. He looked down at her, Arcee was the most beautiful woman he had ever known and she was only one he could ever love. Having noticed his staring, she smiled back as she placed a hand around the back of his neck and gently pulled him down into another passionate kiss as she squeezed her legs around his waist. He then pressed his body down and entered her . She moaned in appreciation as he set a deep steady rhythm with his thrusts. She had never felt such intimacy with another person at all in her life, not in the way that she and Jack were, here as they made love. She was totally in love with him and wanted to stay with him forever as she tightened her grip on his shoulders. Jack then quickened the pace and Arcee returned it in kind as she let another moan slip out from her lips as both of them came close to climax. Jack's vision then went white as he climaxed, followed by Arcee as they both tensed up and let out a loud moan before they collapsed into each others arms while panting heavily. They then just held each other close and looked into each others eyes before succumbing to sleep.

Jack was the first to wake as he looked down at the woman he loved as she lied on him, her head nuzzled against his neck. He turned to see her peaceful expression as her face was completely lax. But then she started stir as her eyes opened and looked at Jack, a smile gracing her lips. "Hi." she said to him completely relaxed as she started to stroke his chest. "Hi" Jack replied.

"By the All-spark Jack, what we just did was incredible." she said, making a wide but loving smile appear on his face. "So were you Arcee" he said gently before they leaned into another kiss. Then Hotrod's voice could be heard over the intercom, interrupting them.

"We are approaching the Refuge system, senior officers to the CIC."

Arcee looked disappointedly at Jack. "Well it was perfect while it lasted." she said coyly as Jack smiled back. "It really was." he replied as they kissed again, this time it lasted longer.

They then broke off and sighed in unison before they reluctantly separated, got up and got dressed.

When they got to the CIC, they found Garrus, Tali and Wrex waiting for them at the Galaxy map. The Turian smiled at them. "Finally, you two took your time." he said. The lovers looked at each other knowingly and then smiled back. "Well we are here now" Jack replied as they walked up to the cockpit where Hotrod was waiting.

"Nice to see your up and about Commander." he replied, gaining a glare from Arcee which put the young Autobot in his place.

"So are we ready for this then?" Jack asked as Tali took a seat at the console next to the pilot. "I have strengthened the shields as much as we can, but we will need to pass through the ion storm as quickly as possible." she replied. Jack then looked back to Hotrod.

"Well if your ready, then take us in." he said and Hotrod nodded as he fired the Normandy's engines and piloted the ship into the waiting ion storm. As the ship flew through the dense storm, electric blasts hitting the ship at every angle but being safely absorbed by it's shields. Each hit made the ship shake some what.

"Shield strength at fifty six percent" Tali responded as Hotrod powered the engines to full and pushed the Normandy through the storm and into the Refuge system.

"We are clear of the ion storm, and shields are holding." Hotrod said as Jack looked at his screen. "Lets see what is out there." he said as Tali made a scan of the system. "I am picking up a single Geth cruiser in the system, orbiting Ilos. No sign of the rest of the fleet or Sovereign."

Hotrod turned to them. "I have already activated stealth mode, so the cruiser hasn't spotted us." he said as Tali completed a scan of the planet. "Scans have found a number of shuttles on Ilos's surface around what appears to be underground entrance. Damn it." she said. Jack stood over her chair and looked down at her console.

"What' the problem Tali?"

She then brought up a map of the Geth landing zone. "It seems the entrance is inside a canyon and is hard to reach, especially since the best LZ is several clicks away."

Jack looked down at the map and smiled. "Then why don't we just drop and shock them." he said with a confident smirk. Tali and Arcee looked at him confused, so Jack decided to explain it. "Drop and shock is an old Alliance combat manoeuvre, we used it back during the Turian first contact troubles."

Garrus then jumped in. "I remember hearing about those."

Jack looked over to his friend. "So you know what I am on about then."

Garrus nodded but the women were still confused. Tali held her hand up. "Still waiting on an explanation here" she said slightly irritated by the two.

"Well, we'll have the Normandy fly down at full speed and when it reaches 600 feet it will release the shuttle which will drop down on top of the Geth so they wont know what hit them."

Arcee looked unsure. "Jack, that canyon is barely wide enough for a shuttle to take such a risk."

Hotrod spun round on his chair to the group. "Hey I can get you down there, definitely." he said beaming with confidence. Jack smiled back at him. "Ok its settled, I want you four suited up and ready in shuttle one. Hotrod, when you are in range drop the stealth mode and blow that cruiser out of the sky and then make the descent. We only have one chance now to get to the conduit before Saren, lets make it happen." He said before turning around heading for the elevator.

"Aye aye Commander" the pilot replied before turning back round to his console. The others following Jack away.

As it approached the brown/yellow planet of Ilos, the Normandy headed straight towards the Geth Cruiser and dropped it's stealth mode as Hotrod activated the ship's torpedoes and cannons. As it got closer the cruiser noticed it and turned to face the Normandy, its own cannons turning to face the alliance vessel.

"Oh no you don't" Hotrod said as he fired the ship's torpedoes which flew away from the Normandy and to the enemy, exploding against the cruiser shields weakening them as they flickered around its hull. Hotrod then fired another volley which then broke through the ship's defences and exploded along its hull.

"Now take this." he said as he aimed the cannons at the cruiser's engines and fired, sending kinetic energy rounds which rained down on the enemy's engines causing it to explode. The Normandy then flew straight past and down towards the planet as the Geth Cruiser exploded, sending its debris in all directions.

At the underground entrance, Saren and Sideways waited at the heavy blast doors as the Geth troops surrounded them. Sideways activated his holo-tool and started hacking the door's locks.

"How long will this take?" Saren said irritated. The former con did not even bother to look up at him as he held his arm up to the door and watched the holographic hacking program spin around his hand. "Should only take a moment."

Then the Turian heard a noise, like a sonic boom in the sky and looked up to see an object far up in its yellow hue, but descending fast. He focused his eyes which then widened in disbelief as he recognised what it was.

"They have found us, get that door open now, he spat as Geth centurions ran in front of the two taking defensive positions.

The Normandy was coming down so fast that Hotrod was continually having to adjust his heading as the ship battled against the G-forces pushing against it.

"We will be in range in 10 seconds, opening landing bay." he said as the door opened to reveal shuttle one ready to launch. The ship then burst through the clouds to reveal the ruins of once mighty city as the ship sped down towards it.

Down on the ground Sideways smiled as his hacking program worked and the blast doors opened to reveal a large tunnel leading into the darkness below.

"Its open." he said as he looked up at what Saren was watching and saw the Normandy getting ever larger as it closed on them.

"Get inside now and you shut these doors once we are in" Saren ordered the Geth in front of him which nodded in return.

The Normandy was now so close that Hotrod launched the shuttle which flew out of the landing bay at the same speed, as the Normandy suddenly veered away and headed back into open space. The Geth on the ground started to fire at the shuttle as it entered the canyon and flew straight at the blast doors which had started to close. The Geth troops didn't even move as the shuttle hit the ground with force and ploughed through them as it slid into the doorway before the blast doors closed and smashed into the walls of the tunnel.

Onboard the crashed shuttle Jack and the others picked themselves up.

"I think that was the worst landing I have ever experienced." Garrus said as he held his hand to his head. "Open the hatch and secure the area while I check on the pilot." Jack ordered ignoring the Turian's moaning as he entered the cockpit and saw the body sprawled over his controls. "Hey, you ok private?" he said as he placed a hand on the pilot's shoulder and pulled back, making the body flop back against his chair revealing his face to be covered in blood. Arcee entered the cockpit. "Is he alright Jack?" she asked as Jack turned to her, his face sad. "No Arcee, he is dead." he replied before looking back at the corpse. "I am sorry, your sacrifice will not be for nothing." he whispered as the femme placed a hand on his shoulder. "He got us down here, now its up to us partner." she said gently as Jack turned back to her, his face now determined. "Lets go".

After they had left the shuttle wreckage and walked down the large tunnel, they came out into a large courtyard like area filled with statues of the Lithone. If the situation wasn't dire then he would have taken the time to look more closely at them. But before they could get any further in, Geth centurions appeared and fired at the team who took cover as the bullets flew over their heads.

"I'm starting to get sick of these things." Garrus shouted as the Acree and Tali fired back, taking out two of the enemies. "Stop complaining Garrus and shoot already." Wrex shot back as he charged over to the next piece of cover, blowing away another Geth with his shotgun along the way. Jack vaulted over his cover and fired his pistol continually in a sweeping motion from left to right, hitting the four Geth in front perfectly in the head as he then brought up his energy blade and sliced clean through the mid section of the Geth closest to him, splitting it in half and its fluid spraying the floor.

"Show off." Garrus called back before raising his sniper rifle and exploding the heads of two Geth who were firing at them from high ground. Arcee and Tali finished off the last of the centurions as Jack and Wrex searched the last pieces of cover to find that there were no more enemies.

"Clear" they both shouted back to the others who nodded.

"Ok, I think that's the last of them" Jack assumed before being hit in the back, making him fall to the floor revealing Sideways standing over him.

"Don't you know that it is the worst thing to say in a situation like this." he gloated as the others raised their weapons at him, Arcee in particular looking at the former con with seething hate. But Sideways didn't even flinch as he pointed his gun at Jack and looked back at them, a confident smirk on his face. "I wouldn't do that if I were you." he threatened them. "Not unless you want me to blow a hole in the back of the Prime's head.".

Arcee and the others immediately lowered their weapons, Sideways noticing the concerned look on her face as his smile grew larger. "Thank you, but anyway…" he said tightening his grip on the trigger, but suddenly flew forward as Jack swept the former con off his feet and kicked his gun away leaving the con to their mercy, as he raised his hands to them in a none threatening pose.

"I surrender, your not going to shoot an unarmed man are you." he pleaded as Jack looked down at him, with his gun aimed at his head.

"No I wont, but she would." he replied as he stepped out of the way and Arcee fired three shots into the former cons chest. He gasped in pain as fluid spilled out of his wounds on to the floor, his body going limp as it too hit the floor. Arcee then stood over his body, her face stoic as Jack joined her. "You ok?" he asked. She looked to him and smiled. "I'm fine partner, its been a long time since I killed a Decepticon." she replied as Jack took her hand in his.

"Come on, we've got to move." he said gently as he then looked over at Tali. "Can you stay here and see what you can find out from the Geth's memory core."

Tali nodded and started scanning the dead Geth with her Holo-tool as the rest walked down the corridor leading out of the area.

They then walked through to another area where they saw Saren and some Geth standing next to a large device.

"Saren!" Jack shouted as they started to run at him, but the Turian just smiled at them as the Geth closed the doors to the room he was in as a bright light filled it. Jack banged his first against the door in anger as Arcee immediately used her holo-tool to try and hack the door's locks.

"I'll see if I can get these to open, but we might be better of with Tali." she said as Jack put his hand up to his com link.

Tali was just finishing downloading the Geth corpse's memory core when she heard a noise behind her. She spun round, shotgun cocked and ready. But saw nothing in the empty room other than the corpses around her, until her gaze fell on something and her eyes widened as she gasped.

"Tali, come in, its Jack" came the Prime's voice over her com link. She then spoke back as she looked around the room in surprise.

"I have a problem up here." she replied.

"What kind of problem" he responded. She checked everywhere but still had no luck.

"Well it seems Sideways's body has gone missing." she responded, getting a shocked look from Arcee as Jack carried on. "Well just get down here, we need you to hack this door that Saren shut."

The Quarian nodded and headed down the corridor toward them.

Once she had joined them, Tali had started to hack the door as Arcee paced back and forth, her face conflicted. "How did his body disappear, I put three bullets in his spark chamber." she said angrily as Jack turned to her. "Arcee, we can worry about Sideways later, but right now we have to stop Saren." he told her as the doors opened and Tali looked back at them smiling. "Just how good am I?" she asked as Garrus patted her on shoulder. "You're the best Tali."

They then entered the room, weapons ready to find that no one was in there. They all looked confused. "Ok how does someone just disappear from a locked room." Wrex asked. Arcee shrugged as she looked around. "We can ask him and Sideways when we find them." she replied with a slight sarcastic tone. But Jack's eyes fell on an object at the end of the room that looked eerily familiar. "Hey, doesn't that look an awful lot like a space bridge."

Arcee joined him and looked at the object. "Yes it does."

As the group gathered round it, they were then startled by a glowing humanoid hologram appearing before them.

"You are not Lithone, and I do not detect the taint of indoctrination on any of you, not like the other who was in here. Perhaps there is still hope."

Tali looked at it curiously. "It looks like a VI program, a very old one at that."

"Jack stepped forward. "Who are you and why can we all understand your language?" he asked as the hologram looked at him.

"My name is Arblus, I was created to give warnings along with the beacons that we planted around the galaxy for the next cycle to find. And I have been monitoring you since your ship got here and so translated my words into something you can understand."

Everyone stood around the VI as they listened to it. "You are not safe here though, nowhere will be safe if something isn't done to stop them."

"You mean the Reapers" Jack replied.

"Yes, you must break a cycle of death that has gripped the galaxy for millions of years. But to stop it, you must first hear our story and so not make the same mistakes we did. The Citadel is the heart of the galactic society in your cycle as it was for us and every cycle before."

Garrus looked confused. "What do you mean cycle?"

"A cycle is the amount of time it takes the species of the galaxy to evolve to a point before the Reapers return to wipe them out, but please do not interrupt me as time is short and you must hear what I have been programmed to say. The Citadel is a trap, it was created by the Reapers as a means to take control of the Space bridge network that the ancient Cybertronians created. So that they could enter our galaxy from dark space, the empty void between the galaxies and spread out to all the advanced species. They would also lock out the races from the network, effectively bottling them into their own sectors so that they could not mount a reasonable defence. We found this out the hard way when the Reapers took control of the Citadel and kept our colonies isolated. They then picked us off one at a time in a war that lasted one hundred years."

Jack looked at the VI. "But have you must have found something that can help us now?"

The VI just looked at the group. "We found out much later, too late to help us that the Reapers had indoctrinated agents onboard the Citadel and helped a single Reaper called Sovereign to take control of it and allow the Reaper fleet to enter our galaxy."

Jack's eyes widened at the comment. "Just like it has done with Saren now."

"Yes, the one that came through here before you. He is being used by Sovereign as a pawn. We had speculated that Sovereign is a lone member of the Reapers who stays in the galaxy and monitors the young species growth and decides when the time is right to wipe them out. But now I must tell you what we had planned towards the end. During the twilight years of the conflict we managed to build a small scale version of a space bridge that would join to the one on the Citadel, we had never figured out why it was there, but now it had become our only hope of regaining control of the Space bridge network and reorganising our forces. But unfortunately the Reapers arrived at this world and wiped out everyone here before we could do so. I deactivated all of this facility's systems to keep from being detected and sent out an adjusted warning to all the beacons in the hope that someone would find me and stop the Reaper invasion before it occurs." Arblus replied.

"So Saren found out about the Conduit, the space bridge here from the beacon on Virmire. And now he used it to sneak onto the Citadel." Jack replied.

"Yes that is correct. As we speak, Sovereign will be approaching the Citadel while Saren deactivates its defences."

Jack the activated his com link. "Darby to Normandy, Hotrod you there?"

"Right here Commander" the Autobot pilot responded.

"I need the Normandy to send a high alert message to the Alliance and tell them that the Citadel is about to be attacked and send all the ships they can to defend it." Jack replied.

"Ok will do, do you want me to pick you up." Hotrod said over the com.

"No, I want you to go to the Citadel and help in it's defence, we have found alternate transportation." Jack replied as the com remained quiet for a moment.

"Alright, will do. Preparing to leave orbit. Good luck Commander." Hotrod finished.

"You too, Darby out." Jack replied as he deactivated his com link and turned back to Arblus.

"Can you reactivate the conduit and let us through?" he asked as the VI looked on.

"Yes, I will activate it for you now" the VI replied as the conduit came to life and expanded a green vortex in front of them. "I have noticed that you are a Prime, the first Prime my people have ever come across. Perhaps you are the one to end this nightmare before it begins. All you have to do is stop the indoctrinated agent before he gives control of the Citadel to Sovereign. Good luck." The hologram said before fading away in front of them. Jack then turned to his friends. "Right, we know what we have to do, so move out." he told them, his face becoming stoic as they acknowledged and followed him into the large vortex before it shut down, leaving Ilos behind.

Meanwhile the Space bridge in the Serpent Nebula activated and a fleet of Geth Cruisers exited the event horizon in formation, along with the massive black form of the Reaper Sovereign as they moved towards the unsuspecting Citadel station.

**A/N: Well I hoped you enjoyed that, there is only one chapter to go now. So as always, let me know what you thought of this chapter through reviews and private messages. And thank you for Reading.**

**Next Chapter: With the fate of the galaxy at stake, Jackson Prime fights Saren for Control of the Citadel while the Reaper Sovereign and the Geth fleet battles what is left of the Citadel Fleet. **


	10. Chapter 10

**A/N: Here is the final chapter, enjoy!**

**PRIME EFFECT**

**CHAPTER X**

Panic hit the Citadel as the station shook from explosions rattling the hull of the vast space station as the Destiny Ascension, the Council's flagship took the lead with the rest of the Citadel fleet as they met the Geth forces head on. Sovereign held back, seemingly happy to just watch for the moment as the both sides exchanged fire with each other. But little did the defence force know that someone had slipped in the Citadel's back door and was about to strike.

In the Citadel Control room, numerous operators representing each council race were at their stations as the alert sirens blared out. An Asari operator activated the com link.

"Citadel control to Destiny Ascension, come in please."

Onboard the Citadel flagship, the Councillors were overseeing the battle from the bridge as it shook from an other hit from the Geth. An Asari crewmember turned from her station to face Tevos. "Madam Councillor, I am receiving a transmission from Citadel control. They wish to know if you want the Citadel arms closed to protect the station?" she said, stress evident in her voice. The Asari Councillor looked over at the others who nodded in return as the ship shook from yet another impact from the Geth weapons. "Affirmative ensign." she replied as the young Asari turned back to her station. "Citadel control, that is an affirmative, close the arms, seal the Citadel. I repeat seal the Citadel." But she was answered by nothing but static as no answer was received. She turned back to the Councillors with a worried expression on her face. "There is no answer, I could have sworn I had them online a moment ago." she said as the Council leaders looked among each other confused.

"What is going on over there?" Sparatus said angrily. But back at Citadel Control, all the operators were either sprawled over their stations or lying on the floor with smoking bullet holes in the back of their heads as Saren stood in the middle of the room with his weapon equipped and smiling. Taking a moment to relish what he had just done, he then activated his holo-tool and sent a signal out to the battle outside.

Then as the fleets continued to battle each other, Sovereign suddenly began to move towards the station as Two Turian cruisers veered into its path.

"That Geth mother ship….thing, is moving on the Citadel, open fire on it now!."

Both ships fired their cannons on the black behemoth, but had no effect as their energy was simply absorbed by the Reaper's shields. Sovereign then powered up its own weapon which glowed bright red before a beam shot out and cut straight through the first cruiser, splitting it into two pieces. One which hit the other Turian cruiser knocking it directly into the path of the Reaper who flew straight through the crippled ship as it exploded against the black ship's hull harmlessly. Sovereign then carried on towards the Citadel as the Geth ships took defensive formation around it, keeping the rest of the Citadel fleet at bay.

"Oh my goddess, the Citadel arms are closing" Tevos said.

The vast station's arms then closed around Sovereign as it headed toward the Citadel tower turning the station into one long armoured cylinder. The Reaper then landed on the tower, wrapping its five legs around it as energy passed between the Citadel and Sovereign.

Saren, having become satisfied by what he saw on the screens in the control room then turned around and left the room, heading for Council Chamber.

Meanwhile in the Citadel Tower gardens, a number of Geth centurions were standing in front of the space bridge monument when it suddenly activated, a green vortex opening up gaining the their attention. For several seconds nothing happened as the Geth began to slowly lower their weapons. Then Jack and his team emerged from the portal and killed the Geth with perfect precision. The Prime then looked directly at the staircase leading to the Council Chamber before turning back to the others.

"Ok, Saren will have to use the Councillors podium to access the station and hand control to Sovereign so I am heading there now." He said before giving his pistol one last check. Arcee and the others looked to him before noticing the room suddenly fill up with Husks who charged toward the group. Arcee looked at Jack. "Go, we will cover you." she said as Jack suddenly looked conflicted with leaving his friends to fend off the hordes that were charging at them. The others started firing at the Husks, "Jack go, we got this." Garrus yelled back, not taking his eyes off the Husks.

"Take that you bosh'tets!" Tali screamed at the husks as she knocked one back with her shotgun. Jack looked at back at femme. "Arcee I…." but he was cut off by her pulling him close and planting a kiss on his lips, before pulling back and looking into his eyes. "You go get him, partner." she said with a confident smile.

Jack returned the smile. "I'll be back before you know it." he replied before turning and running up the stairs as Arcee went back to the group and began fending off the incoming Husks.

Meanwhile outside the closed Citadel, the Destiny Ascension was surrounded by many Geth ships while the rest of the defence force was scattered.

"This is the Destiny Ascension, we are in desperate need of help. Our shields are failing and weapons offline. Is anyone left."

But the Geth ships just continued to fire at the damaged flag ship with no sign of a reprieve. But suddenly the space bridge activated and the Normandy followed by the Alliance fleet exited the green vortex and immediately started firing on the enemy ships. Aboard the Alliance flagship the 'Ark'. Admiral Bryce stood on the bridge looking out at the battle. "This is Admiral Bryce. Heavy Cruiser group two, assist the Destiny Ascension, all other ships break and attack."

The Normandy and the Alliance fleet then joined the battle as the Geth fleet turned to meet them head on.

Back in the Council Chambers, Saren was at the podium working on the holographic Citadel controls when Jack entered the room, gaining the former Spectre's attention.

"Jackson Prime, you know I warned you what would happen if I saw you again." he said as Jack drew his weapon. "Yeah well, what can I say. I missed you." the Prime replied before noticing something with Saren who grinned back at him. He saw that the Turian now had a more synthetic look about him, with tubes and metal plating on his head and body and his eyes looked more like optics, glowing a bright blue as he stared at the Commander.

"What the hell!" Jack exclaimed as Saren laughed.

"I see your admiring my upgrades" he said as Jack slowly got closer. "You see after our last encounter, I started to think about what you said to me about indoctrination. Sovereign, though noticed that I was starting to have doubts and so upgraded me with implants. I now have no doubts, no fears. I believe completely in my master, Sovereign."

Jack looked at him confused. "Did you just say master?"

Saren cocked his head. "What?" he asked just as confused. Jack continued to slowly walk towards the podium. "You just called Sovereign your master. Can't you see what is happening to you?"

Saren just continued to stare at the young Prime.

"Sovereign saw that you were beginning to question its hold over you. So it then upgrades you, allowing it to control you more effectively." Jack said as he neared the edge of the box towards the podium's catwalk. Saren's optics then went narrow as anger took over. "You are just trying to delay me!" he shouted as he threw a grenade towards Jack, who dived behind the nearest cover as it exploded. Saren then turned back to the console to activate the uplink to the Reaper above them. He was about to press the final sequence when a gunshot echoed and the Turian screamed in pain as he grabbed his hand, looking down at the blooded bullet hole in its center. He then turned angrily to see Jack standing on the podium with his pistol raised at him. "I wouldn't do that if I were you." the Commander said as Saren roared at him and pounced at the Prime, slamming both of them into the ground with a thud.

Back in the Gardens, Arcee and Garrus were keeping the Husks at bay as Wrex went head on in and started throwing the creatures around while Tali had deployed drones to help in holding their ground. Suddenly the Quarian's com link activated and Hotrod's voice answered. "Normandy to Prime's team. Come in, is anyone there?" he said, his voice erratic.

"Tali here Hotrod, Jack is currently engaging Saren." she answered.

"I have a message from Admiral Bryce. We need you to open the Citadel arms so we can attack the Reaper. Can you get to Citadel control?"

Tali took a quick scan of the area to see that every exit other than the one to the Council Chamber was covered by Husks. "That's a negative, we have too many hostiles here." she then began to think as Hot rod got impatient. "You still there?"

Tali then smiled. "Yes and I have an idea, there should be an auxiliary control node around here, now if I can hack into it. I will have access to the mainframe and should be able to open the arms." she answered confidently. "Ok then, I will inform the Admiral, Normandy out."

Tali then got up and tapped Garrus on the should before shooting a husk that got to close."

"What is it Tali, we are rather busy here." He answered.

"I need to find a auxiliary control node. Being ex C-Sec, you should know of one right?" she asked as Wrex charged into three more husks and then stomped on another clearly enjoying himself a little to much.

"Yeah there is one right over there, but the water fountain. But Arcee and myself have to stay here and keep them from Council Chamber." The Turian replied as he shot another creature in the head as the others screamed at him.

"I only need five minutes cover." she replied, with a confident tone.

"Then allow me!" Wrex roared as he charged through the line of Husks between them and the node and blowing one into the others with his shotgun, knocking them over like bowling skittles. Tali then sprinted behind him, taking cover behind the fountain while activating her holo-tool. The Krogan stayed at her side, shooting any husks that got too close while the Turian and Autobot femme held the line against the hordes of enemies trying to enter the Council Chamber.

Jack felt his back hit the ground hard as Saren stood over him and gloated. "I see you haven't learned anything since our last fight."

Jack then kicked out at Saren's crotch which didn't phase the Turian at all. "Really, that's your play?" he laughed as he grabbed Jack's leg and lifted him off the ground and threw him against the podium. Jack winced in pain as he rolled off back onto the floor. '_God, those implants have made him even stronger.'_ he thought as he looked over to see the former Spectre approaching him, his optics glowing. Jack got to his feet and waved him over, taunting him. "Come on, is that all you've got?" he said as a little blood trickled down his chin. Saren just growled as he threw a punch which Jack barely blocked before being hit in the stomach by the Turian's other first, knocking him back against the podium. Saren then grabbed Jack by the throat and lifted him off the ground.

"Why are you a Prime?" he asked angrily as he began to choke the Commander. "You are so weak, did you really think you had a chance against me." he spat while not noticing Jack activating his energy blade and swiping it against the enemy's chest, knocking him back as he released him. The Turian then looked down at the wound and smiled. "Better" he chuckled as he attacked Jack again.

Things were getting hectic in the gardens as Husks kept entering the large room, no matter how many the others killed. Tali was still trying to hack the control node as Wrex and the others kept fighting. Suddenly her holo-tool pinged and the Quarian smiled. " I got it, I am in." she exclaimed as she ran back to the line with Wrex who she had to grab and drag away from the husks.

"So what can you do with that access then?" Garrus asked a little impatiently.

" Watch and learn." she smiled as she used her holo-tool. Suddenly all the fountains in the room began overflow, flooding the room.

"I wouldn't stand in that if I were you." Tali said to Arcee and the others, causing them to get out of the rising water and to the top of the stairs leading to the council chamber. Tali then hit a button on her holo-tool and suddenly the power nodes in the room overloaded causing electricity to spread throughout the room using the water as a conductor, electrifying all the husks there. The four of them watched as the husks lied there in the water, completely incapacitated.

"Nice work Tali." Arcee said giving the young Quarian an encouraging smile. Garrus then looked at the Quarian. "Isn't there something else you have to do? He asked. Tali just kept smiling. "Already done it."

Outside the Destiny Ascension had just been saved by the Heavy cruiser group who had suffered heavy losses from defending her. And the remaining Geth ships had started to scatter. Admiral Bryce looked out and smiled as he saw the Citadel arms opening up and giving them a good look at the Reaper inside. "This is Admiral Bryce to all ships, the Citadel is open. Now attack that Reaper, I repeat attack Sovereign."

Then every ship sped inside the opening arms and fired on the resting Behemoth. The Normandy flew around the black ship and fired its cannons, but still not making so much as a dent.

"Sir, the Reaper's shields are still to strong." Hotrod stated as the rest of the fleet surround the enemy.

"Well keep at it, all ships engage." he answered back as all the ships rained down on the Reaper while it fired back at the ships destroying each one in one shot.

Meanwhile the fight between Jack and Saren had reached a stalemate. The Prime stood between the podium's holographic controls and the Turian.

"Your not getting tired are you Saren, not with all of those upgrades?" Jack taunted.

"Not at all Prime. I will defeat you and give control of the Citadel to Sovereign and then the Reapers will return." he replied with confidence in his voice.

"Not on my watch." Jack replied as the two then grappled.

"Why are you resisting Prime. Organics do have place with the Reapers, leaders like you and myself. Sovereign has been impressed by you, join us and you will survive the purge and help lead the new generation under our rule."

Jack gritted his teeth as Saren bared down on him.

"Never, I would rather die then be like you." he growled as he fought back against the Turian, pushing him back enough to swing his energy blade at Saren's legs, cutting them open. The Turian fell to his knees, as Jack stood over him. "You gave yourself to Sovereign, let it change you. Your nothing but its puppet now."

Saren looked up at him. "I will kill you." he spat as he tried to get up, only to be met by Jack's energy blade impaling him through the chest. Saren coughed up blood as he looked at Jack.

"You asked me why I am a Prime. Its because I will do whatever it takes to protect this galaxy from the likes of you and the Reapers." he answered as he pulled the blade back out, blood gushed out of the wound as Jack then watched the light fade from Saren's optics, as his body then slumped to the ground. The Prime looked down at the fallen Turian for a moment, before turning around and walking over to the Citadel controls. He started typing and closing the uplink to Sovereign when suddenly he heard a familiar voice behind him.

"Jack look out!"

He turned to find Saren's body reanimated and his optics glowing as it swung for him. Jack rolled out of the way to see Arcee and the others running toward him. He looked back as Saren's corpse started to glow with red energy as its flesh burnt away to reveal its now synthetic skeleton standing there at the podium.

"_**You will not stop us human Prime, we will be here long after your corpses have turned to dust." **_Sovereign spoke through the corpse as it charged at Jack. The Prime himself charging back at it.

"Jack!" Arcee cried out as she watched her lover running at the abomination. The Saren husk swung at Jack as he rolled under it's attack and swung at it from behind only to be blocked as it hit back. Only for the Prime to dodge it. It then growled an unholy sound as it then jumped at the young man who swung his blade right for the husk's neck, slicing right through. Saren's head fell off and rolled across the floor before coming to a stop at the edge of the platform. It's optics going dead once and for all. Jack just stood there and panted heavily as the others ran up to him.

"Jack you alright?" Arcee asked, finally getting his attention. "Yeah, I fine, a little bloodied and beaten but.." he then realised. "The fleet."

He turned towards the controls and brought up a screen showing the battle outside.

A moment after the Saren husk's death, a red energy passed through the reaper, making it lose control and slowly drift away from the tower.

"Admiral, Sovereign's shields are down." Hotrod said as the Normandy flew around the Reaper.

"Hit it with everything we've got!" he ordered as all the remaining ships hammered the Reaper with all of their weapons. The Normandy flew high up above the battle and spun around, then dived down towards the enemy. It then fired a full spread of torpedoes which impacted along the central body of the Reaper making it explode, sending debris in all directions as the Alliance frigate flew past.

Back in the Council Chamber, Jack and the others had just witnessed Sovereign's demise via the giant pane glass window, but then Jack's face tensed up as he noticed a large piece of debris heading right for them.

"Run!" he shouted as they all started to run away as the debris impacted the tower causing explosive decompression before a force field erected itself in place.

Rescue teams entered the heavily damaged council chambers which a had a piece of Reaper debris stuck in the middle of the large room. Captain Anderson was leading the search as they all shifted through the rubble, looking for survivors.

"Over here" one of the rescue team called as Anderson and two others joined him moving the blocks of concrete out of the way to reveal Arcee and the others hiding in an archway.

"Its ok, your safe now" Anderson said as the rescuers helped the team out into the open. He looked at all of them. "Where is Commander Darby?" he asked as he noticed all of them, especially Arcee look down at the ground, sadness in their eyes.

"Jack, pushed us into that archway moments before…." she trailed off as her gaze fell on Jack's avenger rifle, snapped in half lying on the ground next to a piece of the dead Reaper, the other half buried under it. Anderson and the others joined her as she walked over and picked it up. Tears welling in her eyes as she held it close to her chest. Anderson was about to speak when something caught his attention from behind the large debris, as a shadow was seen moving. The others looked over when they noticed the Captain, a smile growing on his face as a figure suddenly hobbled out from behind the debris. Arcee looked too, but did not register it yet. But then the figure stepped into the light and Arcee's eyes widened as she dropped the rifle on the ground and ran towards him and jumped into the waiting arms of Jack Darby, who gave her the most passionate kiss as the others smiled and surrounded the two lovers. When they finally broke for air, Arcee looked into Jack's eyes. "Don't ever do that to me again." she said with a large smile as she touched her forehead to his.

"I promise Arcee." he answered as everyone around them applauded.

During the aftermath of the battle, everyone was helping to clear debris and repair the damage done to the Citadel. But inside one of the offices, Commander Darby, Captain Anderson and Admiral Bryce stood with the Councillors.

"Captain, Admiral and of course Commander Darby. We wish to thank the Alliance for its part in defeating the forces of Saren and Sovereign." Tevos said.

"Many humans and Autobots died while protecting the Citadel and this Council." Valern continued. "Their sacrifice will not be forgotten."

Tevos turned to Jack. "And we owe you a great debt Commander, one that we will never be able repay. You not only saved our lives, but the lives of billions from the threat of Sovereign and the Reapers."

Jack held his hand up to stop them. "Forgive me madam Councillor, but the Reapers are still out there. And I intend to find a way to stop them."

Tevos nodded. "We understand Commander, and know that this Council now recognises the Alliance as a full member of our society and we will do whatever we can to aid you in your mission."

Jack nodded and then saluted Anderson and Bryce before leaving the office.

Down at the airlock leading to the Normandy, Arcee was waiting as Jack approached. "So are we ready for launch?" Jack asked as Arcee looked over to him, a smile gracing her lips. "Yes everyone is onboard and we are just waiting for you." she replied as Jack held out a hand, which she took. "Then lets get out of here." he said as the two of them entered the ship.

Once in the CIC, Jack and Arcee were greeted by Tali, Garrus and Wrex as the crew worked at their stations.

"So you guys are staying with us then?" he asked.

"Of course we are Jack, we are not going to let our friends do this alone now." Garrus replied.

Jack looked at each of them. "I just want to thank you guys for all of your help during.." but he was cut of by Wrex. "Yeah, yeah. We can do all of this later, right now we have a galaxy to save." The Krogan slapped the Prime on the shoulder making Jack smile.

"Your right Wrex."

He then activated the inter com. "This is the Commander, we are leaving the Citadel for uncharted space. Our mission is to find a means of protecting the galaxy from the Reaper threat. Assume your stations and prepare for departure." He and Arcee then walked up to Hotrod who as always, was in the cockpit.

"Great job on the Citadel Commander!" the young pilot exclaimed as Jack stood beside him.

"Thanks, I heard you did some great flying while battling Sovereign." Jack replied.

"Yeah I sure did." the Autobot beamed. "So where too Commander?"

Jack then looked out into space in front of him.

"Set course for the Omega Nebula, we will start our search there." the Prime ordered as both he and Arcee looked out at the stars ahead of them, knowing that no matter where they went or what threat they faced. They would easily defeat it as long as they were together.

The Normandy then disconnected from the Citadel docking port and flew out beyond the station's arms and into the green vortex of the space bridge.

**To be continued**

**In**

**PRIME EFFECT 2**

**A/N: Well I hope you enjoyed all this as much as I did writing it. Thank you for reading this story. I have enjoyed reading your messages and reviews. And now I will make a start on the sequel, stay tuned.**

**And once more, thank you :)**


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